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Posted to dev@rya.apache.org by Boris Pelakh <bo...@semanticarts.com> on 2018/12/04 14:19:15 UTC

Dataset not applied to queries

I am in the process of implementing a SPARQL 1.1-compliant endpoint for web.rya so that Rya can be used as a federated repository with RDF4J workbench.

One of requirements is to be able to pass default-graph-uri and named-graph-uri filters external to the query to override the graph filter in the query itself (see https://www.w3.org/TR/sparql11-protocol/#query-operation).

In the sail API this is accomplished by setting the dataset on the query object (see http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.html#setDataset-org.eclipse.rdf4j.query.Dataset-), but that setting does not seem to be honored by the Rya SAIL implementation. Any ideas on where I can start digging to correct this?

(I have also tried wrapping the Rya repository connection in a ContextAwareConnection and setting readContexts, but the effect is the same).

Boris Pelakh
Ontologist, Developer, Software Architect
boris.pelakh@semanticarts.com<ma...@semanticarts.com>
+1-321-243-3804
[SemanticArtsLogo]

Re: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Jürgen Jakobitsch <ju...@semantic-web.com>.

hi there again..

i've pushed our changes to our company fork on github..

my commit is this:
https://github.com/semantic-web-company/incubator-rya/commit/2b788ea84848251ea06951ea3371010e319abfb6

any feedback would be highly welcome (an integration even more :-) )

krj

*Jürgen Jakobitsch*
Senior Technical Consultant
Semantic Web Company GmbH
EU: +43-14021235 <+43%201%204021235>
US: (415) 800-3776
Mobile: +43-676-6212710 <+43%20676%206212710>
https://www.poolparty.biz
https://www.semantic-web.com

*Download E-Book*: Introducing Semantic AI
<https://www.poolparty.biz/machine-learning-meets-semantics/>


Am Mi., 5. Dez. 2018 um 21:00 Uhr schrieb Jürgen Jakobitsch <
juergen.jakobitsch@semantic-web.com>:

> hi, yo it's an older version..
>
> we've already upgraded a couple of versions as well and are integrating
> the sparql endpoint in our own rya fork..
>
> there was hardly any reaction to the fist version, so i'm happy that the
> discussion is starting again.
> i'll make sure to commit our current version during the next days and you
> can have a look at it.
>
> krj
>
> *Jürgen Jakobitsch*
> Senior Technical Consultant
> Semantic Web Company GmbH
> EU: +43-14021235 <+43%201%204021235>
> US: (415) 800-3776
> Mobile: +43-676-6212710 <+43%20676%206212710>
> https://www.poolparty.biz
> https://www.semantic-web.com
>
> *Download E-Book*: Introducing Semantic AI
> <https://www.poolparty.biz/machine-learning-meets-semantics/>
>
>
> Am Mi., 5. Dez. 2018 um 20:12 Uhr schrieb Maxim Kolchin <
> kolchinmax@gmail.com>:
>
>> Hi Jurgen,
>>
>> > hi there, we've implemented the whole sparql endpoint anew.
>>
>> Thank you for the work!
>>
>> But unfortunately, I wasn't able to use the code you published, because
>> it's based on libraries which aren't used in Rya from the master branch,
>> like OpenRDF Sesame which was replaced by RDF4J. Is it because you use an
>> older code base?
>>
>> So I'd spent some time to integrate Rya with RDF4J Workbench and it
>> worked.
>> You can find the code in
>> https://github.com/DataFabricRus/incubator-rya/tree/datafabric-patches.
>> The
>> branch contains a lot of unrelated changes, so it may be hard to find
>> exact
>> changes we've made to integrate RDF4J Workbench, but the starting point is
>> the web module. Maybe it'll help someone.
>>
>> > However, that information is not used when building the Accumulo queries
>> in ParallelEvaluationStrategyImpl.java, which is something I will still
>> need to address.
>>
>> I didn't test that with RDF4J Workbench, so my mail probably unhelpful for
>> you, sorry.
>>
>> Maxim
>>
>> On Wed, Dec 5, 2018 at 8:53 PM Boris Pelakh <
>> boris.pelakh@semanticarts.com>
>> wrote:
>>
>> > Yes, the deficiency in the evaluation engine is the problem I am trying
>> to
>> > address. As per the SPARQL 1.1. protocol, the default-graph-uri and
>> > named-graph-uri query parameters are supposed to override any graph
>> names
>> > provided in the query itself. The Rdf4j workbench, which provides a very
>> > nice web UI, uses the options to implement some of its navigation
>> > functionality.
>> >
>> > The RDF4J SAIL interface implemented by Rya provides for this exact
>> > functionality by allowing the specification of a Dataset on any query
>> > object. However, that information is not used when building the Accumulo
>> > queries in ParallelEvaluationStrategyImpl.java, which is something I
>> will
>> > still need to address.
>> >
>> > Boris Pelakh
>> > Ontologist, Developer, Software Architect
>> > boris.pelakh@semanticarts.com
>> > +1-321-243-3804
>> >
>> >
>> > -----Original Message-----
>> > From: Jürgen Jakobitsch <ju...@semantic-web.com>
>> > Sent: Wednesday, December 5, 2018 12:19 PM
>> > To: dev@rya.incubator.apache.org
>> > Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
>> >
>> > no, i didn't include that parameter..
>> >
>> > usually this parameter is anyway included in the SPARQL query itself as
>> > FROM or FROM NAMED.
>> >
>> > mind that depending on the situation you might have to rewrite the
>> query..
>> >
>> > also mind that there are some application specifics involved, since we
>> > also have DEFAULT keyword in SPARQL and finally also mind that the
>> > evaluation strategy (the actual SPARQL engine here) must make use of the
>> > graph constraint, which i think isn't done at the moment
>> >
>> > krj
>> >
>> >
>> > *Jürgen Jakobitsch*
>> > Senior Technical Consultant
>> > Semantic Web Company GmbH
>> > EU: +43-14021235 <+43%201%204021235>
>> > US: (415) 800-3776
>> > Mobile: +43-676-6212710 <+43%20676%206212710> https://www.poolparty.biz
>> > https://www.semantic-web.com
>> >
>> > *Download E-Book*: Introducing Semantic AI <
>> > https://www.poolparty.biz/machine-learning-meets-semantics/>
>> >
>> >
>> > Am Mi., 5. Dez. 2018 um 17:56 Uhr schrieb Boris Pelakh <
>> > boris.pelakh@semanticarts.com>:
>> >
>> > > Hi, Jurgen
>> > >
>> > > I looked at your source, and you do not appear to have addressed the
>> > > default-graph-uri and named-graph-uri constraints defined in the
>> > > SPARQL 1.1 protocol
>> > > (https://www.w3.org/TR/sparql11-protocol/#protocol). Is this
>> addressed
>> > somewhere other than SPARQLController.java?
>> > >
>> > > Boris Pelakh
>> > > Ontologist, Developer, Software Architect
>> > > boris.pelakh@semanticarts.com
>> > > +1-321-243-3804
>> > >
>> > >
>> > > -----Original Message-----
>> > > From: Jürgen Jakobitsch <ju...@semantic-web.com>
>> > > Sent: Wednesday, December 5, 2018 10:45 AM
>> > > To: dev@rya.incubator.apache.org
>> > > Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
>> > >
>> > > hi there, we've implemented the whole sparql endpoint anew.
>> > >
>> > > some of the features from the old endpoint are still missing, but i
>> > > think they need some re-engineering anyway, like send a user as a url
>> > > paramter is not exactly a good idea..
>> > >
>> > > i'm including a mail from i wrote from earlier this year (around
>> > > april/may)
>> > >
>> > > hi,
>> > >
>> > > as mentioned in previous mails, we've setup a first draft of the
>> > > proposed upgrade of rya's sparql endpoint.. again note, that we've
>> > > setup a small debug/demo maven project using a sesame memory store to
>> > > demonstrate the proposed changes. if the proposed upgrade of the
>> > > sparql endpoint is welcome we would incorporate this with existing rya
>> > > code to include all required rya features.
>> > > features:
>> > >
>> > > 1. full support for content-negotiation (essential within the
>> > > linkeddata/semantic web realm) 2. SPARQL Service Description 3. more
>> > > HTTP Status Codes (202 accepted, 400 bad request, 200 ok) 4. all RDF
>> > > serialization formats available natively from sesame 5. customizable
>> > > web endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
>> > > + Styles)
>> > > 6. valid XHTML for the endpoint
>> > > 7. valid XHTML+RDFa in a browser for construct queries 8. a future
>> > > rdf4j upgrade will not seriously affect the whole endpoint
>> > >
>> > > the project is very easy to build and you can checkout all features on
>> > > your local machine easily (examples are provided). the maven build
>> > > will include a tomcat hosting this sample endpoint, descriptions and
>> > > code can be found
>> > > here:
>> > >
>> > > https://github.com/jj-semantic-web-com/rya-sparql-endpoint
>> > >
>> > > any feedback, pointers, comments and wishes are highly welcome!
>> > >
>> > > related JIRA task: https://issues.apache.org/jira/browse/RYA-477
>> > >
>> > > kr jürgen
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > *Jürgen Jakobitsch*
>> > > Senior Technical Consultant
>> > > Semantic Web Company GmbH
>> > > EU: +43-14021235 <+43%201%204021235>
>> > > US: (415) 800-3776
>> > > Mobile: +43-676-6212710 <+43%20676%206212710>
>> > > https://www.poolparty.biz https://www.semantic-web.com
>> > >
>> > > *Download E-Book*: Introducing Semantic AI <
>> > > https://www.poolparty.biz/machine-learning-meets-semantics/>
>> > >
>> > >
>> > > Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu <
>> > > adina@usna.edu
>> > > >:
>> > >
>> > > > Hi Jurgen,
>> > > >
>> > > > If you see this message, can you please reply?
>> > > >
>> > > > Boris, if you create a JIRA account you should be able to add
>> > > > comments and "watch" the issue to be notified of changes.
>> > > >
>> > > > Adina
>> > > > On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh
>> > > > <boris.pelakh@semanticarts.com
>> > > > >
>> > > > wrote:
>> > > >
>> > > > > Hi, Adina,
>> > > > >
>> > > > >
>> > > > > Thanks for the pointer, and I wish I had seen this prior to
>> > > > > starting my effort. My work is essentially complete with the
>> > > > > exception of the aforementioned defect in applying default and
>> > > > > named graph filters, and it covers pretty much that entire Jira
>> > > > > issue. I have no way of contacting Jurgen, as I only have read
>> > > > > access to the JIRA instance you linked, but
>> > > > it
>> > > > > seems that no work has been done on that 'In Progress' issue for
>> > > > > more
>> > > > than
>> > > > > 6 months.
>> > > > >
>> > > > >
>> > > > > Boris
>> > > > >
>> > > > > ________________________________
>> > > > > From: Adina Crainiceanu <ad...@usna.edu>
>> > > > > Sent: Wednesday, December 5, 2018 9:32:17 AM
>> > > > > To: dev@rya.incubator.apache.org
>> > > > > Subject: Re: Dataset not applied to queries
>> > > > >
>> > > > > Hi Boris,
>> > > > >
>> > > > > There is some work currently being done on the SPARQL endpoint by
>> > > > > Jurgen
>> > > > in
>> > > > > RYA-477 https://issues.apache.org/jira/browse/RYA-477
>> > > > > Let's make sure we discuss there ideas and design decisions on the
>> > > > > dev list. I would hate if someone's work gets duplicated. In
>> > > > > general, please check whether a JIRA issue for the bug/desired
>> > > > > feature does not already exist
>> > > > > https://issues.apache.org/jira/browse/RYA. If it does,
>> collaborate
>> > > > > with the person assigned to that issue (if any) or assign the
>> > > > > issue to yourself (if none assigned). If not, create the issue and
>> > > > > assign it to yourself. If you cannot assign an issue to yourself,
>> > > > > send a message to
>> > > > the
>> > > > > dev list with the Jira username, so you can be added to the list
>> > > > > of contributors in JIRA.
>> > > > >
>> > > > > Looking forward to your contributions!
>> > > > > Adina
>> > > > >
>> > > > >
>> > > > >
>> > > > > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com>
>> > > wrote:
>> > > > >
>> > > > > > I can definitely take a look, but Aaron would also be a good
>> > > > > > person if
>> > > > > its
>> > > > > > mostly using Accumulo backed Rya.  You're touching core Rya
>> > > > > > classes so
>> > > > > the
>> > > > > > more eyes the better!
>> > > > > >
>> > > > > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
>> > > > > > boris.pelakh@semanticarts.com>
>> > > > > > wrote:
>> > > > > >
>> > > > > > > Thanks, Puja, that's very helpful. I am making the changes in
>> > > > > > > a
>> > > > forked
>> > > > > > > repo, would I assign pull requests to you once I am finished?
>> > > > > > >
>> > > > > > > Boris Pelakh
>> > > > > > > Ontologist, Developer, Software Architect
>> > > > > > > boris.pelakh@semanticarts.com
>> > > > > > > +1-321-243-3804
>> > > > > > >
>> > > > > > >
>> > > > > > > -----Original Message-----
>> > > > > > > From: Puja Valiyil <pu...@gmail.com>
>> > > > > > > Sent: Tuesday, December 4, 2018 10:12 AM
>> > > > > > > To: dev@rya.incubator.apache.org
>> > > > > > > Subject: Re: Dataset not applied to queries
>> > > > > > >
>> > > > > > > Hi Boris,
>> > > > > > > The execution of the query plan is done by the
>> > > > > > ParallelEvaluationStrategy:
>> > > > > > >
>> > > > > > >
>> > > > > >
>> > > > >
>> > > >
>> https://github.com/apache/incubator-rya/blob/master/sail/src/main/ja
>> > > > va
>> > > > /org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategy
>> > > > Im
>> > > > pl.java
>> > > > > > >
>> > > > > > > It looks like whoever did the rdf4j upgrade updated that class
>> > > > > > > to
>> > > > take
>> > > > > > the
>> > > > > > > dataset object in its constructor, but it doesn't seem to be
>> > > > > > > used
>> > > > > > anywhere
>> > > > > > > in query evaluation.  That would be the class to modify,  but
>> > > > > > > I'm
>> > > > still
>> > > > > > not
>> > > > > > > clear on what the changes would look like since I'm not
>> > > > > > > familiar with
>> > > > > > what
>> > > > > > > the contract is supposed to be.
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
>> > > > > > boris.pelakh@semanticarts.com
>> > > > > > > >
>> > > > > > > wrote:
>> > > > > > >
>> > > > > > > > So, a
>> > > > > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
>> > > > > > > > is logically equivalent to
>> > > > > > > >
>> > > > > > > > SELECT ...
>> > > > > > > > FROM <my-named-graph>
>> > > > > > > > WHERE ...
>> > > > > > > >
>> > > > > > > > (overriding whatever FROM/FROM NAMED clauses actually
>> > > > > > > > specified in
>> > > > > the
>> > > > > > > > query) I looked at
>> > > > > > > >
>> > > > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evalua
>> > > > > te
>> > > > > In
>> > > > > > > > ternal(), and the dataset containing the overriding graph
>> > > > > > > > names is passed in, but does not seem to be honored, i.e if
>> > > > > > > > I have the following data:
>> > > > > > > >
>> > > > > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
>> > > > > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
>> > > > > > > >
>> > > > > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }'
>> > > > > > > > with default-graph-uri set to ns:g1, I expect to get 1, but
>> I
>> > get 2.
>> > > > > > > >
>> > > > > > > > I am assuming that there is someplace where the TupleExpr
>> > > > > > > > passed to evaluateInternal gets transformed into a scan
>> > > > > > > > pattern for Accumulo, after the right index (spo/ops/pso) is
>> > > > > > > > identified. If I remember correctly, S/P/O is used the the
>> > > > > > > > row ID, and the graph is the
>> > > > column
>> > > > > > > > name (or family?). So the dataset should modify the scan
>> > > > > > > > filter if
>> > > > > > > applied correctly.
>> > > > > > > >
>> > > > > > > > Boris Pelakh
>> > > > > > > > Ontologist, Developer, Software Architect
>> > > > > > > > boris.pelakh@semanticarts.com
>> > > > > > > > +1-321-243-3804
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Puja Valiyil <pu...@gmail.com>
>> > > > > > > > Sent: Tuesday, December 4, 2018 9:31 AM
>> > > > > > > > To: dev@rya.incubator.apache.org
>> > > > > > > > Subject: Re: Dataset not applied to queries
>> > > > > > > >
>> > > > > > > > Hi Boris,
>> > > > > > > > Unfortunately I'm not very familiar with that method -- can
>> > > > > > > > you provide some more details into exactly what its supposed
>> > > > > > > > to
>> > > do?
>> > > > > > > > All of the connectors for implementing the sail api are in
>> > > > > > > > the rya.sail, and the main classes to look at are
>> > > > > > > > RdfCloudTripleStore, RyaSailRepository, and
>> > > > > > > > RdfCloudTripleStoreConnection. All of these classes all
>> > > > > > > > extend abstract implementations SAIL provides out of
>> > > > the
>> > > > > > > > box, so typically the way you extend them to do more stuff
>> > > > > > > > is to
>> > > > look
>> > > > > > > > at the Sail implementation and customize it for Rya's data
>> > > > > structures.
>> > > > > > > > If you need any help or want to bounce any implementation
>> > > > > > > > ideas off
>> > > > > of
>> > > > > > > > anyone, please send out an email over the dev list. Just let
>> > > > > > > > us
>> > > > know
>> > > > > > > > how we can help!
>> > > > > > > > Thanks,
>> > > > > > > > Puja
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
>> > > > > > > > <boris.pelakh@semanticarts.com
>> > > > > > > > >
>> > > > > > > > wrote:
>> > > > > > > >
>> > > > > > > > > I am in the process of implementing a SPARQL 1.1-compliant
>> > > > endpoint
>> > > > > > > > > for web.rya so that Rya can be used as a federated
>> > > > > > > > > repository
>> > > > with
>> > > > > > > > > RDF4J workbench.
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > > One of requirements is to be able to pass
>> > > > > > > > > default-graph-uri and named-graph-uri filters external to
>> > > > > > > > > the query to override the
>> > > > graph
>> > > > > > > > > filter in the query itself (see
>> > > > > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation
>> ).
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > > In the sail API this is accomplished by setting the
>> > > > > > > > > dataset on
>> > > > the
>> > > > > > > > > query object (see
>> > > > > > > > >
>> > > > >
>> http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
>> > > > > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
>> > > > > > > > > but that setting does not seem to be honored by the Rya
>> > > > > > > > > SAIL implementation. Any ideas on where I can start
>> > > > > > > > > digging to correct
>> > > > > > this?
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > > (I have also tried wrapping the Rya repository connection
>> > > > > > > > > in a ContextAwareConnection and setting readContexts, but
>> > > > > > > > > the effect
>> > > > is
>> > > > > > > > > the same).
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > > *Boris Pelakh*
>> > > > > > > > >
>> > > > > > > > > *Ontologist, Developer, Software Architect*
>> > > > > > > > >
>> > > > > > > > > *boris.pelakh@semanticarts.com
>> > > > > > > > > <bo...@semanticarts.com>*
>> > > > > > > > >
>> > > > > > > > > *+1-321-243-3804*
>> > > > > > > > >
>> > > > > > > > > [image: SemanticArtsLogo]
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > > >
>> > > > > > > >
>> > > > > > >
>> > > > > >
>> > > > >
>> > > > >
>> > > > > --
>> > > > > Dr. Adina Crainiceanu
>> > > > > Associate Professor
>> > > > > Computer Science Department
>> > > > > United States Naval Academy
>> > > > > 410-293-6822
>> > > > > adina@usna.edu
>> > > > > http://www.usna.edu/Users/cs/adina/
>> > > > >
>> > > >
>> > > >
>> > > > --
>> > > > Dr. Adina Crainiceanu
>> > > > Associate Professor
>> > > > Computer Science Department
>> > > > United States Naval Academy
>> > > > 410-293-6822
>> > > > adina@usna.edu
>> > > > http://www.usna.edu/Users/cs/adina/
>> > > >
>> > >
>> >
>>
>

Re: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Jürgen Jakobitsch <ju...@semantic-web.com>.

hi, yo it's an older version..

we've already upgraded a couple of versions as well and are integrating the
sparql endpoint in our own rya fork..

there was hardly any reaction to the fist version, so i'm happy that the
discussion is starting again.
i'll make sure to commit our current version during the next days and you
can have a look at it.

krj

*Jürgen Jakobitsch*
Senior Technical Consultant
Semantic Web Company GmbH
EU: +43-14021235 <+43%201%204021235>
US: (415) 800-3776
Mobile: +43-676-6212710 <+43%20676%206212710>
https://www.poolparty.biz
https://www.semantic-web.com

*Download E-Book*: Introducing Semantic AI
<https://www.poolparty.biz/machine-learning-meets-semantics/>


Am Mi., 5. Dez. 2018 um 20:12 Uhr schrieb Maxim Kolchin <
kolchinmax@gmail.com>:

> Hi Jurgen,
>
> > hi there, we've implemented the whole sparql endpoint anew.
>
> Thank you for the work!
>
> But unfortunately, I wasn't able to use the code you published, because
> it's based on libraries which aren't used in Rya from the master branch,
> like OpenRDF Sesame which was replaced by RDF4J. Is it because you use an
> older code base?
>
> So I'd spent some time to integrate Rya with RDF4J Workbench and it worked.
> You can find the code in
> https://github.com/DataFabricRus/incubator-rya/tree/datafabric-patches.
> The
> branch contains a lot of unrelated changes, so it may be hard to find exact
> changes we've made to integrate RDF4J Workbench, but the starting point is
> the web module. Maybe it'll help someone.
>
> > However, that information is not used when building the Accumulo queries
> in ParallelEvaluationStrategyImpl.java, which is something I will still
> need to address.
>
> I didn't test that with RDF4J Workbench, so my mail probably unhelpful for
> you, sorry.
>
> Maxim
>
> On Wed, Dec 5, 2018 at 8:53 PM Boris Pelakh <boris.pelakh@semanticarts.com
> >
> wrote:
>
> > Yes, the deficiency in the evaluation engine is the problem I am trying
> to
> > address. As per the SPARQL 1.1. protocol, the default-graph-uri and
> > named-graph-uri query parameters are supposed to override any graph names
> > provided in the query itself. The Rdf4j workbench, which provides a very
> > nice web UI, uses the options to implement some of its navigation
> > functionality.
> >
> > The RDF4J SAIL interface implemented by Rya provides for this exact
> > functionality by allowing the specification of a Dataset on any query
> > object. However, that information is not used when building the Accumulo
> > queries in ParallelEvaluationStrategyImpl.java, which is something I will
> > still need to address.
> >
> > Boris Pelakh
> > Ontologist, Developer, Software Architect
> > boris.pelakh@semanticarts.com
> > +1-321-243-3804
> >
> >
> > -----Original Message-----
> > From: Jürgen Jakobitsch <ju...@semantic-web.com>
> > Sent: Wednesday, December 5, 2018 12:19 PM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
> >
> > no, i didn't include that parameter..
> >
> > usually this parameter is anyway included in the SPARQL query itself as
> > FROM or FROM NAMED.
> >
> > mind that depending on the situation you might have to rewrite the
> query..
> >
> > also mind that there are some application specifics involved, since we
> > also have DEFAULT keyword in SPARQL and finally also mind that the
> > evaluation strategy (the actual SPARQL engine here) must make use of the
> > graph constraint, which i think isn't done at the moment
> >
> > krj
> >
> >
> > *Jürgen Jakobitsch*
> > Senior Technical Consultant
> > Semantic Web Company GmbH
> > EU: +43-14021235 <+43%201%204021235>
> > US: (415) 800-3776
> > Mobile: +43-676-6212710 <+43%20676%206212710> https://www.poolparty.biz
> > https://www.semantic-web.com
> >
> > *Download E-Book*: Introducing Semantic AI <
> > https://www.poolparty.biz/machine-learning-meets-semantics/>
> >
> >
> > Am Mi., 5. Dez. 2018 um 17:56 Uhr schrieb Boris Pelakh <
> > boris.pelakh@semanticarts.com>:
> >
> > > Hi, Jurgen
> > >
> > > I looked at your source, and you do not appear to have addressed the
> > > default-graph-uri and named-graph-uri constraints defined in the
> > > SPARQL 1.1 protocol
> > > (https://www.w3.org/TR/sparql11-protocol/#protocol). Is this addressed
> > somewhere other than SPARQLController.java?
> > >
> > > Boris Pelakh
> > > Ontologist, Developer, Software Architect
> > > boris.pelakh@semanticarts.com
> > > +1-321-243-3804
> > >
> > >
> > > -----Original Message-----
> > > From: Jürgen Jakobitsch <ju...@semantic-web.com>
> > > Sent: Wednesday, December 5, 2018 10:45 AM
> > > To: dev@rya.incubator.apache.org
> > > Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
> > >
> > > hi there, we've implemented the whole sparql endpoint anew.
> > >
> > > some of the features from the old endpoint are still missing, but i
> > > think they need some re-engineering anyway, like send a user as a url
> > > paramter is not exactly a good idea..
> > >
> > > i'm including a mail from i wrote from earlier this year (around
> > > april/may)
> > >
> > > hi,
> > >
> > > as mentioned in previous mails, we've setup a first draft of the
> > > proposed upgrade of rya's sparql endpoint.. again note, that we've
> > > setup a small debug/demo maven project using a sesame memory store to
> > > demonstrate the proposed changes. if the proposed upgrade of the
> > > sparql endpoint is welcome we would incorporate this with existing rya
> > > code to include all required rya features.
> > > features:
> > >
> > > 1. full support for content-negotiation (essential within the
> > > linkeddata/semantic web realm) 2. SPARQL Service Description 3. more
> > > HTTP Status Codes (202 accepted, 400 bad request, 200 ok) 4. all RDF
> > > serialization formats available natively from sesame 5. customizable
> > > web endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
> > > + Styles)
> > > 6. valid XHTML for the endpoint
> > > 7. valid XHTML+RDFa in a browser for construct queries 8. a future
> > > rdf4j upgrade will not seriously affect the whole endpoint
> > >
> > > the project is very easy to build and you can checkout all features on
> > > your local machine easily (examples are provided). the maven build
> > > will include a tomcat hosting this sample endpoint, descriptions and
> > > code can be found
> > > here:
> > >
> > > https://github.com/jj-semantic-web-com/rya-sparql-endpoint
> > >
> > > any feedback, pointers, comments and wishes are highly welcome!
> > >
> > > related JIRA task: https://issues.apache.org/jira/browse/RYA-477
> > >
> > > kr jürgen
> > >
> > >
> > >
> > >
> > >
> > > *Jürgen Jakobitsch*
> > > Senior Technical Consultant
> > > Semantic Web Company GmbH
> > > EU: +43-14021235 <+43%201%204021235>
> > > US: (415) 800-3776
> > > Mobile: +43-676-6212710 <+43%20676%206212710>
> > > https://www.poolparty.biz https://www.semantic-web.com
> > >
> > > *Download E-Book*: Introducing Semantic AI <
> > > https://www.poolparty.biz/machine-learning-meets-semantics/>
> > >
> > >
> > > Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu <
> > > adina@usna.edu
> > > >:
> > >
> > > > Hi Jurgen,
> > > >
> > > > If you see this message, can you please reply?
> > > >
> > > > Boris, if you create a JIRA account you should be able to add
> > > > comments and "watch" the issue to be notified of changes.
> > > >
> > > > Adina
> > > > On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh
> > > > <boris.pelakh@semanticarts.com
> > > > >
> > > > wrote:
> > > >
> > > > > Hi, Adina,
> > > > >
> > > > >
> > > > > Thanks for the pointer, and I wish I had seen this prior to
> > > > > starting my effort. My work is essentially complete with the
> > > > > exception of the aforementioned defect in applying default and
> > > > > named graph filters, and it covers pretty much that entire Jira
> > > > > issue. I have no way of contacting Jurgen, as I only have read
> > > > > access to the JIRA instance you linked, but
> > > > it
> > > > > seems that no work has been done on that 'In Progress' issue for
> > > > > more
> > > > than
> > > > > 6 months.
> > > > >
> > > > >
> > > > > Boris
> > > > >
> > > > > ________________________________
> > > > > From: Adina Crainiceanu <ad...@usna.edu>
> > > > > Sent: Wednesday, December 5, 2018 9:32:17 AM
> > > > > To: dev@rya.incubator.apache.org
> > > > > Subject: Re: Dataset not applied to queries
> > > > >
> > > > > Hi Boris,
> > > > >
> > > > > There is some work currently being done on the SPARQL endpoint by
> > > > > Jurgen
> > > > in
> > > > > RYA-477 https://issues.apache.org/jira/browse/RYA-477
> > > > > Let's make sure we discuss there ideas and design decisions on the
> > > > > dev list. I would hate if someone's work gets duplicated. In
> > > > > general, please check whether a JIRA issue for the bug/desired
> > > > > feature does not already exist
> > > > > https://issues.apache.org/jira/browse/RYA. If it does, collaborate
> > > > > with the person assigned to that issue (if any) or assign the
> > > > > issue to yourself (if none assigned). If not, create the issue and
> > > > > assign it to yourself. If you cannot assign an issue to yourself,
> > > > > send a message to
> > > > the
> > > > > dev list with the Jira username, so you can be added to the list
> > > > > of contributors in JIRA.
> > > > >
> > > > > Looking forward to your contributions!
> > > > > Adina
> > > > >
> > > > >
> > > > >
> > > > > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com>
> > > wrote:
> > > > >
> > > > > > I can definitely take a look, but Aaron would also be a good
> > > > > > person if
> > > > > its
> > > > > > mostly using Accumulo backed Rya.  You're touching core Rya
> > > > > > classes so
> > > > > the
> > > > > > more eyes the better!
> > > > > >
> > > > > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> > > > > > boris.pelakh@semanticarts.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Thanks, Puja, that's very helpful. I am making the changes in
> > > > > > > a
> > > > forked
> > > > > > > repo, would I assign pull requests to you once I am finished?
> > > > > > >
> > > > > > > Boris Pelakh
> > > > > > > Ontologist, Developer, Software Architect
> > > > > > > boris.pelakh@semanticarts.com
> > > > > > > +1-321-243-3804
> > > > > > >
> > > > > > >
> > > > > > > -----Original Message-----
> > > > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > > > > > To: dev@rya.incubator.apache.org
> > > > > > > Subject: Re: Dataset not applied to queries
> > > > > > >
> > > > > > > Hi Boris,
> > > > > > > The execution of the query plan is done by the
> > > > > > ParallelEvaluationStrategy:
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > https://github.com/apache/incubator-rya/blob/master/sail/src/main/ja
> > > > va
> > > > /org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategy
> > > > Im
> > > > pl.java
> > > > > > >
> > > > > > > It looks like whoever did the rdf4j upgrade updated that class
> > > > > > > to
> > > > take
> > > > > > the
> > > > > > > dataset object in its constructor, but it doesn't seem to be
> > > > > > > used
> > > > > > anywhere
> > > > > > > in query evaluation.  That would be the class to modify,  but
> > > > > > > I'm
> > > > still
> > > > > > not
> > > > > > > clear on what the changes would look like since I'm not
> > > > > > > familiar with
> > > > > > what
> > > > > > > the contract is supposed to be.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > > > > > boris.pelakh@semanticarts.com
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > So, a
> > > > > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > > > > > is logically equivalent to
> > > > > > > >
> > > > > > > > SELECT ...
> > > > > > > > FROM <my-named-graph>
> > > > > > > > WHERE ...
> > > > > > > >
> > > > > > > > (overriding whatever FROM/FROM NAMED clauses actually
> > > > > > > > specified in
> > > > > the
> > > > > > > > query) I looked at
> > > > > > > >
> > > > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evalua
> > > > > te
> > > > > In
> > > > > > > > ternal(), and the dataset containing the overriding graph
> > > > > > > > names is passed in, but does not seem to be honored, i.e if
> > > > > > > > I have the following data:
> > > > > > > >
> > > > > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > > > > > >
> > > > > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }'
> > > > > > > > with default-graph-uri set to ns:g1, I expect to get 1, but I
> > get 2.
> > > > > > > >
> > > > > > > > I am assuming that there is someplace where the TupleExpr
> > > > > > > > passed to evaluateInternal gets transformed into a scan
> > > > > > > > pattern for Accumulo, after the right index (spo/ops/pso) is
> > > > > > > > identified. If I remember correctly, S/P/O is used the the
> > > > > > > > row ID, and the graph is the
> > > > column
> > > > > > > > name (or family?). So the dataset should modify the scan
> > > > > > > > filter if
> > > > > > > applied correctly.
> > > > > > > >
> > > > > > > > Boris Pelakh
> > > > > > > > Ontologist, Developer, Software Architect
> > > > > > > > boris.pelakh@semanticarts.com
> > > > > > > > +1-321-243-3804
> > > > > > > >
> > > > > > > >
> > > > > > > > -----Original Message-----
> > > > > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > > > > > To: dev@rya.incubator.apache.org
> > > > > > > > Subject: Re: Dataset not applied to queries
> > > > > > > >
> > > > > > > > Hi Boris,
> > > > > > > > Unfortunately I'm not very familiar with that method -- can
> > > > > > > > you provide some more details into exactly what its supposed
> > > > > > > > to
> > > do?
> > > > > > > > All of the connectors for implementing the sail api are in
> > > > > > > > the rya.sail, and the main classes to look at are
> > > > > > > > RdfCloudTripleStore, RyaSailRepository, and
> > > > > > > > RdfCloudTripleStoreConnection. All of these classes all
> > > > > > > > extend abstract implementations SAIL provides out of
> > > > the
> > > > > > > > box, so typically the way you extend them to do more stuff
> > > > > > > > is to
> > > > look
> > > > > > > > at the Sail implementation and customize it for Rya's data
> > > > > structures.
> > > > > > > > If you need any help or want to bounce any implementation
> > > > > > > > ideas off
> > > > > of
> > > > > > > > anyone, please send out an email over the dev list. Just let
> > > > > > > > us
> > > > know
> > > > > > > > how we can help!
> > > > > > > > Thanks,
> > > > > > > > Puja
> > > > > > > >
> > > > > > > >
> > > > > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > > > > > > <boris.pelakh@semanticarts.com
> > > > > > > > >
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > I am in the process of implementing a SPARQL 1.1-compliant
> > > > endpoint
> > > > > > > > > for web.rya so that Rya can be used as a federated
> > > > > > > > > repository
> > > > with
> > > > > > > > > RDF4J workbench.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > One of requirements is to be able to pass
> > > > > > > > > default-graph-uri and named-graph-uri filters external to
> > > > > > > > > the query to override the
> > > > graph
> > > > > > > > > filter in the query itself (see
> > > > > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > In the sail API this is accomplished by setting the
> > > > > > > > > dataset on
> > > > the
> > > > > > > > > query object (see
> > > > > > > > >
> > > > >
> http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > > > > > but that setting does not seem to be honored by the Rya
> > > > > > > > > SAIL implementation. Any ideas on where I can start
> > > > > > > > > digging to correct
> > > > > > this?
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > (I have also tried wrapping the Rya repository connection
> > > > > > > > > in a ContextAwareConnection and setting readContexts, but
> > > > > > > > > the effect
> > > > is
> > > > > > > > > the same).
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > *Boris Pelakh*
> > > > > > > > >
> > > > > > > > > *Ontologist, Developer, Software Architect*
> > > > > > > > >
> > > > > > > > > *boris.pelakh@semanticarts.com
> > > > > > > > > <bo...@semanticarts.com>*
> > > > > > > > >
> > > > > > > > > *+1-321-243-3804*
> > > > > > > > >
> > > > > > > > > [image: SemanticArtsLogo]
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Dr. Adina Crainiceanu
> > > > > Associate Professor
> > > > > Computer Science Department
> > > > > United States Naval Academy
> > > > > 410-293-6822
> > > > > adina@usna.edu
> > > > > http://www.usna.edu/Users/cs/adina/
> > > > >
> > > >
> > > >
> > > > --
> > > > Dr. Adina Crainiceanu
> > > > Associate Professor
> > > > Computer Science Department
> > > > United States Naval Academy
> > > > 410-293-6822
> > > > adina@usna.edu
> > > > http://www.usna.edu/Users/cs/adina/
> > > >
> > >
> >
>

Re: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Maxim Kolchin <ko...@gmail.com>.

Hi Jurgen,

> hi there, we've implemented the whole sparql endpoint anew.

Thank you for the work!

But unfortunately, I wasn't able to use the code you published, because
it's based on libraries which aren't used in Rya from the master branch,
like OpenRDF Sesame which was replaced by RDF4J. Is it because you use an
older code base?

So I'd spent some time to integrate Rya with RDF4J Workbench and it worked.
You can find the code in
https://github.com/DataFabricRus/incubator-rya/tree/datafabric-patches. The
branch contains a lot of unrelated changes, so it may be hard to find exact
changes we've made to integrate RDF4J Workbench, but the starting point is
the web module. Maybe it'll help someone.

> However, that information is not used when building the Accumulo queries
in ParallelEvaluationStrategyImpl.java, which is something I will still
need to address.

I didn't test that with RDF4J Workbench, so my mail probably unhelpful for
you, sorry.

Maxim

On Wed, Dec 5, 2018 at 8:53 PM Boris Pelakh <bo...@semanticarts.com>
wrote:

> Yes, the deficiency in the evaluation engine is the problem I am trying to
> address. As per the SPARQL 1.1. protocol, the default-graph-uri and
> named-graph-uri query parameters are supposed to override any graph names
> provided in the query itself. The Rdf4j workbench, which provides a very
> nice web UI, uses the options to implement some of its navigation
> functionality.
>
> The RDF4J SAIL interface implemented by Rya provides for this exact
> functionality by allowing the specification of a Dataset on any query
> object. However, that information is not used when building the Accumulo
> queries in ParallelEvaluationStrategyImpl.java, which is something I will
> still need to address.
>
> Boris Pelakh
> Ontologist, Developer, Software Architect
> boris.pelakh@semanticarts.com
> +1-321-243-3804
>
>
> -----Original Message-----
> From: Jürgen Jakobitsch <ju...@semantic-web.com>
> Sent: Wednesday, December 5, 2018 12:19 PM
> To: dev@rya.incubator.apache.org
> Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
>
> no, i didn't include that parameter..
>
> usually this parameter is anyway included in the SPARQL query itself as
> FROM or FROM NAMED.
>
> mind that depending on the situation you might have to rewrite the query..
>
> also mind that there are some application specifics involved, since we
> also have DEFAULT keyword in SPARQL and finally also mind that the
> evaluation strategy (the actual SPARQL engine here) must make use of the
> graph constraint, which i think isn't done at the moment
>
> krj
>
>
> *Jürgen Jakobitsch*
> Senior Technical Consultant
> Semantic Web Company GmbH
> EU: +43-14021235 <+43%201%204021235>
> US: (415) 800-3776
> Mobile: +43-676-6212710 <+43%20676%206212710> https://www.poolparty.biz
> https://www.semantic-web.com
>
> *Download E-Book*: Introducing Semantic AI <
> https://www.poolparty.biz/machine-learning-meets-semantics/>
>
>
> Am Mi., 5. Dez. 2018 um 17:56 Uhr schrieb Boris Pelakh <
> boris.pelakh@semanticarts.com>:
>
> > Hi, Jurgen
> >
> > I looked at your source, and you do not appear to have addressed the
> > default-graph-uri and named-graph-uri constraints defined in the
> > SPARQL 1.1 protocol
> > (https://www.w3.org/TR/sparql11-protocol/#protocol). Is this addressed
> somewhere other than SPARQLController.java?
> >
> > Boris Pelakh
> > Ontologist, Developer, Software Architect
> > boris.pelakh@semanticarts.com
> > +1-321-243-3804
> >
> >
> > -----Original Message-----
> > From: Jürgen Jakobitsch <ju...@semantic-web.com>
> > Sent: Wednesday, December 5, 2018 10:45 AM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
> >
> > hi there, we've implemented the whole sparql endpoint anew.
> >
> > some of the features from the old endpoint are still missing, but i
> > think they need some re-engineering anyway, like send a user as a url
> > paramter is not exactly a good idea..
> >
> > i'm including a mail from i wrote from earlier this year (around
> > april/may)
> >
> > hi,
> >
> > as mentioned in previous mails, we've setup a first draft of the
> > proposed upgrade of rya's sparql endpoint.. again note, that we've
> > setup a small debug/demo maven project using a sesame memory store to
> > demonstrate the proposed changes. if the proposed upgrade of the
> > sparql endpoint is welcome we would incorporate this with existing rya
> > code to include all required rya features.
> > features:
> >
> > 1. full support for content-negotiation (essential within the
> > linkeddata/semantic web realm) 2. SPARQL Service Description 3. more
> > HTTP Status Codes (202 accepted, 400 bad request, 200 ok) 4. all RDF
> > serialization formats available natively from sesame 5. customizable
> > web endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
> > + Styles)
> > 6. valid XHTML for the endpoint
> > 7. valid XHTML+RDFa in a browser for construct queries 8. a future
> > rdf4j upgrade will not seriously affect the whole endpoint
> >
> > the project is very easy to build and you can checkout all features on
> > your local machine easily (examples are provided). the maven build
> > will include a tomcat hosting this sample endpoint, descriptions and
> > code can be found
> > here:
> >
> > https://github.com/jj-semantic-web-com/rya-sparql-endpoint
> >
> > any feedback, pointers, comments and wishes are highly welcome!
> >
> > related JIRA task: https://issues.apache.org/jira/browse/RYA-477
> >
> > kr jürgen
> >
> >
> >
> >
> >
> > *Jürgen Jakobitsch*
> > Senior Technical Consultant
> > Semantic Web Company GmbH
> > EU: +43-14021235 <+43%201%204021235>
> > US: (415) 800-3776
> > Mobile: +43-676-6212710 <+43%20676%206212710>
> > https://www.poolparty.biz https://www.semantic-web.com
> >
> > *Download E-Book*: Introducing Semantic AI <
> > https://www.poolparty.biz/machine-learning-meets-semantics/>
> >
> >
> > Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu <
> > adina@usna.edu
> > >:
> >
> > > Hi Jurgen,
> > >
> > > If you see this message, can you please reply?
> > >
> > > Boris, if you create a JIRA account you should be able to add
> > > comments and "watch" the issue to be notified of changes.
> > >
> > > Adina
> > > On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh
> > > <boris.pelakh@semanticarts.com
> > > >
> > > wrote:
> > >
> > > > Hi, Adina,
> > > >
> > > >
> > > > Thanks for the pointer, and I wish I had seen this prior to
> > > > starting my effort. My work is essentially complete with the
> > > > exception of the aforementioned defect in applying default and
> > > > named graph filters, and it covers pretty much that entire Jira
> > > > issue. I have no way of contacting Jurgen, as I only have read
> > > > access to the JIRA instance you linked, but
> > > it
> > > > seems that no work has been done on that 'In Progress' issue for
> > > > more
> > > than
> > > > 6 months.
> > > >
> > > >
> > > > Boris
> > > >
> > > > ________________________________
> > > > From: Adina Crainiceanu <ad...@usna.edu>
> > > > Sent: Wednesday, December 5, 2018 9:32:17 AM
> > > > To: dev@rya.incubator.apache.org
> > > > Subject: Re: Dataset not applied to queries
> > > >
> > > > Hi Boris,
> > > >
> > > > There is some work currently being done on the SPARQL endpoint by
> > > > Jurgen
> > > in
> > > > RYA-477 https://issues.apache.org/jira/browse/RYA-477
> > > > Let's make sure we discuss there ideas and design decisions on the
> > > > dev list. I would hate if someone's work gets duplicated. In
> > > > general, please check whether a JIRA issue for the bug/desired
> > > > feature does not already exist
> > > > https://issues.apache.org/jira/browse/RYA. If it does, collaborate
> > > > with the person assigned to that issue (if any) or assign the
> > > > issue to yourself (if none assigned). If not, create the issue and
> > > > assign it to yourself. If you cannot assign an issue to yourself,
> > > > send a message to
> > > the
> > > > dev list with the Jira username, so you can be added to the list
> > > > of contributors in JIRA.
> > > >
> > > > Looking forward to your contributions!
> > > > Adina
> > > >
> > > >
> > > >
> > > > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com>
> > wrote:
> > > >
> > > > > I can definitely take a look, but Aaron would also be a good
> > > > > person if
> > > > its
> > > > > mostly using Accumulo backed Rya.  You're touching core Rya
> > > > > classes so
> > > > the
> > > > > more eyes the better!
> > > > >
> > > > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> > > > > boris.pelakh@semanticarts.com>
> > > > > wrote:
> > > > >
> > > > > > Thanks, Puja, that's very helpful. I am making the changes in
> > > > > > a
> > > forked
> > > > > > repo, would I assign pull requests to you once I am finished?
> > > > > >
> > > > > > Boris Pelakh
> > > > > > Ontologist, Developer, Software Architect
> > > > > > boris.pelakh@semanticarts.com
> > > > > > +1-321-243-3804
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > > > > To: dev@rya.incubator.apache.org
> > > > > > Subject: Re: Dataset not applied to queries
> > > > > >
> > > > > > Hi Boris,
> > > > > > The execution of the query plan is done by the
> > > > > ParallelEvaluationStrategy:
> > > > > >
> > > > > >
> > > > >
> > > >
> > > https://github.com/apache/incubator-rya/blob/master/sail/src/main/ja
> > > va
> > > /org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategy
> > > Im
> > > pl.java
> > > > > >
> > > > > > It looks like whoever did the rdf4j upgrade updated that class
> > > > > > to
> > > take
> > > > > the
> > > > > > dataset object in its constructor, but it doesn't seem to be
> > > > > > used
> > > > > anywhere
> > > > > > in query evaluation.  That would be the class to modify,  but
> > > > > > I'm
> > > still
> > > > > not
> > > > > > clear on what the changes would look like since I'm not
> > > > > > familiar with
> > > > > what
> > > > > > the contract is supposed to be.
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > > > > boris.pelakh@semanticarts.com
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > So, a
> > > > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > > > > is logically equivalent to
> > > > > > >
> > > > > > > SELECT ...
> > > > > > > FROM <my-named-graph>
> > > > > > > WHERE ...
> > > > > > >
> > > > > > > (overriding whatever FROM/FROM NAMED clauses actually
> > > > > > > specified in
> > > > the
> > > > > > > query) I looked at
> > > > > > >
> > > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evalua
> > > > te
> > > > In
> > > > > > > ternal(), and the dataset containing the overriding graph
> > > > > > > names is passed in, but does not seem to be honored, i.e if
> > > > > > > I have the following data:
> > > > > > >
> > > > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > > > > >
> > > > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }'
> > > > > > > with default-graph-uri set to ns:g1, I expect to get 1, but I
> get 2.
> > > > > > >
> > > > > > > I am assuming that there is someplace where the TupleExpr
> > > > > > > passed to evaluateInternal gets transformed into a scan
> > > > > > > pattern for Accumulo, after the right index (spo/ops/pso) is
> > > > > > > identified. If I remember correctly, S/P/O is used the the
> > > > > > > row ID, and the graph is the
> > > column
> > > > > > > name (or family?). So the dataset should modify the scan
> > > > > > > filter if
> > > > > > applied correctly.
> > > > > > >
> > > > > > > Boris Pelakh
> > > > > > > Ontologist, Developer, Software Architect
> > > > > > > boris.pelakh@semanticarts.com
> > > > > > > +1-321-243-3804
> > > > > > >
> > > > > > >
> > > > > > > -----Original Message-----
> > > > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > > > > To: dev@rya.incubator.apache.org
> > > > > > > Subject: Re: Dataset not applied to queries
> > > > > > >
> > > > > > > Hi Boris,
> > > > > > > Unfortunately I'm not very familiar with that method -- can
> > > > > > > you provide some more details into exactly what its supposed
> > > > > > > to
> > do?
> > > > > > > All of the connectors for implementing the sail api are in
> > > > > > > the rya.sail, and the main classes to look at are
> > > > > > > RdfCloudTripleStore, RyaSailRepository, and
> > > > > > > RdfCloudTripleStoreConnection. All of these classes all
> > > > > > > extend abstract implementations SAIL provides out of
> > > the
> > > > > > > box, so typically the way you extend them to do more stuff
> > > > > > > is to
> > > look
> > > > > > > at the Sail implementation and customize it for Rya's data
> > > > structures.
> > > > > > > If you need any help or want to bounce any implementation
> > > > > > > ideas off
> > > > of
> > > > > > > anyone, please send out an email over the dev list. Just let
> > > > > > > us
> > > know
> > > > > > > how we can help!
> > > > > > > Thanks,
> > > > > > > Puja
> > > > > > >
> > > > > > >
> > > > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > > > > > <boris.pelakh@semanticarts.com
> > > > > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > I am in the process of implementing a SPARQL 1.1-compliant
> > > endpoint
> > > > > > > > for web.rya so that Rya can be used as a federated
> > > > > > > > repository
> > > with
> > > > > > > > RDF4J workbench.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > One of requirements is to be able to pass
> > > > > > > > default-graph-uri and named-graph-uri filters external to
> > > > > > > > the query to override the
> > > graph
> > > > > > > > filter in the query itself (see
> > > > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > In the sail API this is accomplished by setting the
> > > > > > > > dataset on
> > > the
> > > > > > > > query object (see
> > > > > > > >
> > > > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > > > > but that setting does not seem to be honored by the Rya
> > > > > > > > SAIL implementation. Any ideas on where I can start
> > > > > > > > digging to correct
> > > > > this?
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > (I have also tried wrapping the Rya repository connection
> > > > > > > > in a ContextAwareConnection and setting readContexts, but
> > > > > > > > the effect
> > > is
> > > > > > > > the same).
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > *Boris Pelakh*
> > > > > > > >
> > > > > > > > *Ontologist, Developer, Software Architect*
> > > > > > > >
> > > > > > > > *boris.pelakh@semanticarts.com
> > > > > > > > <bo...@semanticarts.com>*
> > > > > > > >
> > > > > > > > *+1-321-243-3804*
> > > > > > > >
> > > > > > > > [image: SemanticArtsLogo]
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Dr. Adina Crainiceanu
> > > > Associate Professor
> > > > Computer Science Department
> > > > United States Naval Academy
> > > > 410-293-6822
> > > > adina@usna.edu
> > > > http://www.usna.edu/Users/cs/adina/
> > > >
> > >
> > >
> > > --
> > > Dr. Adina Crainiceanu
> > > Associate Professor
> > > Computer Science Department
> > > United States Naval Academy
> > > 410-293-6822
> > > adina@usna.edu
> > > http://www.usna.edu/Users/cs/adina/
> > >
> >
>

RE: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Boris Pelakh <bo...@semanticarts.com>.

Yes, the deficiency in the evaluation engine is the problem I am trying to address. As per the SPARQL 1.1. protocol, the default-graph-uri and named-graph-uri query parameters are supposed to override any graph names provided in the query itself. The Rdf4j workbench, which provides a very nice web UI, uses the options to implement some of its navigation functionality.

The RDF4J SAIL interface implemented by Rya provides for this exact functionality by allowing the specification of a Dataset on any query object. However, that information is not used when building the Accumulo queries in ParallelEvaluationStrategyImpl.java, which is something I will still need to address.

Boris Pelakh
Ontologist, Developer, Software Architect
boris.pelakh@semanticarts.com
+1-321-243-3804


-----Original Message-----
From: Jürgen Jakobitsch <ju...@semantic-web.com> 
Sent: Wednesday, December 5, 2018 12:19 PM
To: dev@rya.incubator.apache.org
Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]

no, i didn't include that parameter..

usually this parameter is anyway included in the SPARQL query itself as FROM or FROM NAMED.

mind that depending on the situation you might have to rewrite the query..

also mind that there are some application specifics involved, since we also have DEFAULT keyword in SPARQL and finally also mind that the evaluation strategy (the actual SPARQL engine here) must make use of the graph constraint, which i think isn't done at the moment

krj


*Jürgen Jakobitsch*
Senior Technical Consultant
Semantic Web Company GmbH
EU: +43-14021235 <+43%201%204021235>
US: (415) 800-3776
Mobile: +43-676-6212710 <+43%20676%206212710> https://www.poolparty.biz https://www.semantic-web.com

*Download E-Book*: Introducing Semantic AI <https://www.poolparty.biz/machine-learning-meets-semantics/>


Am Mi., 5. Dez. 2018 um 17:56 Uhr schrieb Boris Pelakh <
boris.pelakh@semanticarts.com>:

> Hi, Jurgen
>
> I looked at your source, and you do not appear to have addressed the 
> default-graph-uri and named-graph-uri constraints defined in the 
> SPARQL 1.1 protocol 
> (https://www.w3.org/TR/sparql11-protocol/#protocol). Is this addressed somewhere other than SPARQLController.java?
>
> Boris Pelakh
> Ontologist, Developer, Software Architect 
> boris.pelakh@semanticarts.com
> +1-321-243-3804
>
>
> -----Original Message-----
> From: Jürgen Jakobitsch <ju...@semantic-web.com>
> Sent: Wednesday, December 5, 2018 10:45 AM
> To: dev@rya.incubator.apache.org
> Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
>
> hi there, we've implemented the whole sparql endpoint anew.
>
> some of the features from the old endpoint are still missing, but i 
> think they need some re-engineering anyway, like send a user as a url 
> paramter is not exactly a good idea..
>
> i'm including a mail from i wrote from earlier this year (around 
> april/may)
>
> hi,
>
> as mentioned in previous mails, we've setup a first draft of the 
> proposed upgrade of rya's sparql endpoint.. again note, that we've 
> setup a small debug/demo maven project using a sesame memory store to 
> demonstrate the proposed changes. if the proposed upgrade of the 
> sparql endpoint is welcome we would incorporate this with existing rya 
> code to include all required rya features.
> features:
>
> 1. full support for content-negotiation (essential within the 
> linkeddata/semantic web realm) 2. SPARQL Service Description 3. more 
> HTTP Status Codes (202 accepted, 400 bad request, 200 ok) 4. all RDF 
> serialization formats available natively from sesame 5. customizable 
> web endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
> + Styles)
> 6. valid XHTML for the endpoint
> 7. valid XHTML+RDFa in a browser for construct queries 8. a future 
> rdf4j upgrade will not seriously affect the whole endpoint
>
> the project is very easy to build and you can checkout all features on 
> your local machine easily (examples are provided). the maven build 
> will include a tomcat hosting this sample endpoint, descriptions and 
> code can be found
> here:
>
> https://github.com/jj-semantic-web-com/rya-sparql-endpoint
>
> any feedback, pointers, comments and wishes are highly welcome!
>
> related JIRA task: https://issues.apache.org/jira/browse/RYA-477
>
> kr jürgen
>
>
>
>
>
> *Jürgen Jakobitsch*
> Senior Technical Consultant
> Semantic Web Company GmbH
> EU: +43-14021235 <+43%201%204021235>
> US: (415) 800-3776
> Mobile: +43-676-6212710 <+43%20676%206212710> 
> https://www.poolparty.biz https://www.semantic-web.com
>
> *Download E-Book*: Introducing Semantic AI < 
> https://www.poolparty.biz/machine-learning-meets-semantics/>
>
>
> Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu < 
> adina@usna.edu
> >:
>
> > Hi Jurgen,
> >
> > If you see this message, can you please reply?
> >
> > Boris, if you create a JIRA account you should be able to add 
> > comments and "watch" the issue to be notified of changes.
> >
> > Adina
> > On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh 
> > <boris.pelakh@semanticarts.com
> > >
> > wrote:
> >
> > > Hi, Adina,
> > >
> > >
> > > Thanks for the pointer, and I wish I had seen this prior to 
> > > starting my effort. My work is essentially complete with the 
> > > exception of the aforementioned defect in applying default and 
> > > named graph filters, and it covers pretty much that entire Jira 
> > > issue. I have no way of contacting Jurgen, as I only have read 
> > > access to the JIRA instance you linked, but
> > it
> > > seems that no work has been done on that 'In Progress' issue for 
> > > more
> > than
> > > 6 months.
> > >
> > >
> > > Boris
> > >
> > > ________________________________
> > > From: Adina Crainiceanu <ad...@usna.edu>
> > > Sent: Wednesday, December 5, 2018 9:32:17 AM
> > > To: dev@rya.incubator.apache.org
> > > Subject: Re: Dataset not applied to queries
> > >
> > > Hi Boris,
> > >
> > > There is some work currently being done on the SPARQL endpoint by 
> > > Jurgen
> > in
> > > RYA-477 https://issues.apache.org/jira/browse/RYA-477
> > > Let's make sure we discuss there ideas and design decisions on the 
> > > dev list. I would hate if someone's work gets duplicated. In 
> > > general, please check whether a JIRA issue for the bug/desired 
> > > feature does not already exist 
> > > https://issues.apache.org/jira/browse/RYA. If it does, collaborate 
> > > with the person assigned to that issue (if any) or assign the 
> > > issue to yourself (if none assigned). If not, create the issue and 
> > > assign it to yourself. If you cannot assign an issue to yourself, 
> > > send a message to
> > the
> > > dev list with the Jira username, so you can be added to the list 
> > > of contributors in JIRA.
> > >
> > > Looking forward to your contributions!
> > > Adina
> > >
> > >
> > >
> > > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com>
> wrote:
> > >
> > > > I can definitely take a look, but Aaron would also be a good 
> > > > person if
> > > its
> > > > mostly using Accumulo backed Rya.  You're touching core Rya 
> > > > classes so
> > > the
> > > > more eyes the better!
> > > >
> > > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh < 
> > > > boris.pelakh@semanticarts.com>
> > > > wrote:
> > > >
> > > > > Thanks, Puja, that's very helpful. I am making the changes in 
> > > > > a
> > forked
> > > > > repo, would I assign pull requests to you once I am finished?
> > > > >
> > > > > Boris Pelakh
> > > > > Ontologist, Developer, Software Architect 
> > > > > boris.pelakh@semanticarts.com
> > > > > +1-321-243-3804
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > > > To: dev@rya.incubator.apache.org
> > > > > Subject: Re: Dataset not applied to queries
> > > > >
> > > > > Hi Boris,
> > > > > The execution of the query plan is done by the
> > > > ParallelEvaluationStrategy:
> > > > >
> > > > >
> > > >
> > >
> > https://github.com/apache/incubator-rya/blob/master/sail/src/main/ja
> > va 
> > /org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategy
> > Im
> > pl.java
> > > > >
> > > > > It looks like whoever did the rdf4j upgrade updated that class 
> > > > > to
> > take
> > > > the
> > > > > dataset object in its constructor, but it doesn't seem to be 
> > > > > used
> > > > anywhere
> > > > > in query evaluation.  That would be the class to modify,  but 
> > > > > I'm
> > still
> > > > not
> > > > > clear on what the changes would look like since I'm not 
> > > > > familiar with
> > > > what
> > > > > the contract is supposed to be.
> > > > >
> > > > >
> > > > >
> > > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > > > boris.pelakh@semanticarts.com
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > So, a
> > > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > > > is logically equivalent to
> > > > > >
> > > > > > SELECT ...
> > > > > > FROM <my-named-graph>
> > > > > > WHERE ...
> > > > > >
> > > > > > (overriding whatever FROM/FROM NAMED clauses actually 
> > > > > > specified in
> > > the
> > > > > > query) I looked at
> > > > > >
> > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evalua
> > > te
> > > In
> > > > > > ternal(), and the dataset containing the overriding graph 
> > > > > > names is passed in, but does not seem to be honored, i.e if 
> > > > > > I have the following data:
> > > > > >
> > > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > > > >
> > > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' 
> > > > > > with default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > > > > >
> > > > > > I am assuming that there is someplace where the TupleExpr 
> > > > > > passed to evaluateInternal gets transformed into a scan 
> > > > > > pattern for Accumulo, after the right index (spo/ops/pso) is 
> > > > > > identified. If I remember correctly, S/P/O is used the the 
> > > > > > row ID, and the graph is the
> > column
> > > > > > name (or family?). So the dataset should modify the scan 
> > > > > > filter if
> > > > > applied correctly.
> > > > > >
> > > > > > Boris Pelakh
> > > > > > Ontologist, Developer, Software Architect 
> > > > > > boris.pelakh@semanticarts.com
> > > > > > +1-321-243-3804
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > > > To: dev@rya.incubator.apache.org
> > > > > > Subject: Re: Dataset not applied to queries
> > > > > >
> > > > > > Hi Boris,
> > > > > > Unfortunately I'm not very familiar with that method -- can 
> > > > > > you provide some more details into exactly what its supposed 
> > > > > > to
> do?
> > > > > > All of the connectors for implementing the sail api are in 
> > > > > > the rya.sail, and the main classes to look at are 
> > > > > > RdfCloudTripleStore, RyaSailRepository, and 
> > > > > > RdfCloudTripleStoreConnection. All of these classes all 
> > > > > > extend abstract implementations SAIL provides out of
> > the
> > > > > > box, so typically the way you extend them to do more stuff 
> > > > > > is to
> > look
> > > > > > at the Sail implementation and customize it for Rya's data
> > > structures.
> > > > > > If you need any help or want to bounce any implementation 
> > > > > > ideas off
> > > of
> > > > > > anyone, please send out an email over the dev list. Just let 
> > > > > > us
> > know
> > > > > > how we can help!
> > > > > > Thanks,
> > > > > > Puja
> > > > > >
> > > > > >
> > > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh 
> > > > > > <boris.pelakh@semanticarts.com
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > I am in the process of implementing a SPARQL 1.1-compliant
> > endpoint
> > > > > > > for web.rya so that Rya can be used as a federated 
> > > > > > > repository
> > with
> > > > > > > RDF4J workbench.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > One of requirements is to be able to pass 
> > > > > > > default-graph-uri and named-graph-uri filters external to 
> > > > > > > the query to override the
> > graph
> > > > > > > filter in the query itself (see 
> > > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > In the sail API this is accomplished by setting the 
> > > > > > > dataset on
> > the
> > > > > > > query object (see
> > > > > > >
> > > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > > > but that setting does not seem to be honored by the Rya 
> > > > > > > SAIL implementation. Any ideas on where I can start 
> > > > > > > digging to correct
> > > > this?
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > (I have also tried wrapping the Rya repository connection 
> > > > > > > in a ContextAwareConnection and setting readContexts, but 
> > > > > > > the effect
> > is
> > > > > > > the same).
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > *Boris Pelakh*
> > > > > > >
> > > > > > > *Ontologist, Developer, Software Architect*
> > > > > > >
> > > > > > > *boris.pelakh@semanticarts.com
> > > > > > > <bo...@semanticarts.com>*
> > > > > > >
> > > > > > > *+1-321-243-3804*
> > > > > > >
> > > > > > > [image: SemanticArtsLogo]
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Dr. Adina Crainiceanu
> > > Associate Professor
> > > Computer Science Department
> > > United States Naval Academy
> > > 410-293-6822
> > > adina@usna.edu
> > > http://www.usna.edu/Users/cs/adina/
> > >
> >
> >
> > --
> > Dr. Adina Crainiceanu
> > Associate Professor
> > Computer Science Department
> > United States Naval Academy
> > 410-293-6822
> > adina@usna.edu
> > http://www.usna.edu/Users/cs/adina/
> >
>

Re: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Jürgen Jakobitsch <ju...@semantic-web.com>.

no, i didn't include that parameter..

usually this parameter is anyway included in the SPARQL query itself as
FROM or FROM NAMED.

mind that depending on the situation you might have to rewrite the query..

also mind that there are some application specifics involved, since we also
have DEFAULT keyword in SPARQL and finally also mind
that the evaluation strategy (the actual SPARQL engine here) must make use
of the graph constraint, which i think isn't done at the moment

krj


*Jürgen Jakobitsch*
Senior Technical Consultant
Semantic Web Company GmbH
EU: +43-14021235 <+43%201%204021235>
US: (415) 800-3776
Mobile: +43-676-6212710 <+43%20676%206212710>
https://www.poolparty.biz
https://www.semantic-web.com

*Download E-Book*: Introducing Semantic AI
<https://www.poolparty.biz/machine-learning-meets-semantics/>


Am Mi., 5. Dez. 2018 um 17:56 Uhr schrieb Boris Pelakh <
boris.pelakh@semanticarts.com>:

> Hi, Jurgen
>
> I looked at your source, and you do not appear to have addressed the
> default-graph-uri and named-graph-uri constraints defined in the SPARQL 1.1
> protocol (https://www.w3.org/TR/sparql11-protocol/#protocol). Is this
> addressed somewhere other than SPARQLController.java?
>
> Boris Pelakh
> Ontologist, Developer, Software Architect
> boris.pelakh@semanticarts.com
> +1-321-243-3804
>
>
> -----Original Message-----
> From: Jürgen Jakobitsch <ju...@semantic-web.com>
> Sent: Wednesday, December 5, 2018 10:45 AM
> To: dev@rya.incubator.apache.org
> Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]
>
> hi there, we've implemented the whole sparql endpoint anew.
>
> some of the features from the old endpoint are still missing, but i think
> they need some re-engineering anyway, like send a user as a url paramter is
> not exactly a good idea..
>
> i'm including a mail from i wrote from earlier this year (around april/may)
>
> hi,
>
> as mentioned in previous mails, we've setup a first draft of the proposed
> upgrade of rya's sparql endpoint.. again note, that we've setup a small
> debug/demo maven project using a sesame memory store to demonstrate the
> proposed changes. if the proposed upgrade of the sparql endpoint is welcome
> we would incorporate this with existing rya code to include all required
> rya features.
> features:
>
> 1. full support for content-negotiation (essential within the
> linkeddata/semantic web realm) 2. SPARQL Service Description 3. more HTTP
> Status Codes (202 accepted, 400 bad request, 200 ok) 4. all RDF
> serialization formats available natively from sesame 5. customizable web
> endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
> + Styles)
> 6. valid XHTML for the endpoint
> 7. valid XHTML+RDFa in a browser for construct queries 8. a future rdf4j
> upgrade will not seriously affect the whole endpoint
>
> the project is very easy to build and you can checkout all features on
> your local machine easily (examples are provided). the maven build will
> include a tomcat hosting this sample endpoint, descriptions and code can be
> found
> here:
>
> https://github.com/jj-semantic-web-com/rya-sparql-endpoint
>
> any feedback, pointers, comments and wishes are highly welcome!
>
> related JIRA task: https://issues.apache.org/jira/browse/RYA-477
>
> kr jürgen
>
>
>
>
>
> *Jürgen Jakobitsch*
> Senior Technical Consultant
> Semantic Web Company GmbH
> EU: +43-14021235 <+43%201%204021235>
> US: (415) 800-3776
> Mobile: +43-676-6212710 <+43%20676%206212710> https://www.poolparty.biz
> https://www.semantic-web.com
>
> *Download E-Book*: Introducing Semantic AI <
> https://www.poolparty.biz/machine-learning-meets-semantics/>
>
>
> Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu <
> adina@usna.edu
> >:
>
> > Hi Jurgen,
> >
> > If you see this message, can you please reply?
> >
> > Boris, if you create a JIRA account you should be able to add comments
> > and "watch" the issue to be notified of changes.
> >
> > Adina
> > On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh
> > <boris.pelakh@semanticarts.com
> > >
> > wrote:
> >
> > > Hi, Adina,
> > >
> > >
> > > Thanks for the pointer, and I wish I had seen this prior to starting
> > > my effort. My work is essentially complete with the exception of the
> > > aforementioned defect in applying default and named graph filters,
> > > and it covers pretty much that entire Jira issue. I have no way of
> > > contacting Jurgen, as I only have read access to the JIRA instance
> > > you linked, but
> > it
> > > seems that no work has been done on that 'In Progress' issue for
> > > more
> > than
> > > 6 months.
> > >
> > >
> > > Boris
> > >
> > > ________________________________
> > > From: Adina Crainiceanu <ad...@usna.edu>
> > > Sent: Wednesday, December 5, 2018 9:32:17 AM
> > > To: dev@rya.incubator.apache.org
> > > Subject: Re: Dataset not applied to queries
> > >
> > > Hi Boris,
> > >
> > > There is some work currently being done on the SPARQL endpoint by
> > > Jurgen
> > in
> > > RYA-477 https://issues.apache.org/jira/browse/RYA-477
> > > Let's make sure we discuss there ideas and design decisions on the
> > > dev list. I would hate if someone's work gets duplicated. In
> > > general, please check whether a JIRA issue for the bug/desired
> > > feature does not already exist
> > > https://issues.apache.org/jira/browse/RYA. If it does, collaborate
> > > with the person assigned to that issue (if any) or assign the issue
> > > to yourself (if none assigned). If not, create the issue and assign
> > > it to yourself. If you cannot assign an issue to yourself, send a
> > > message to
> > the
> > > dev list with the Jira username, so you can be added to the list of
> > > contributors in JIRA.
> > >
> > > Looking forward to your contributions!
> > > Adina
> > >
> > >
> > >
> > > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com>
> wrote:
> > >
> > > > I can definitely take a look, but Aaron would also be a good
> > > > person if
> > > its
> > > > mostly using Accumulo backed Rya.  You're touching core Rya
> > > > classes so
> > > the
> > > > more eyes the better!
> > > >
> > > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> > > > boris.pelakh@semanticarts.com>
> > > > wrote:
> > > >
> > > > > Thanks, Puja, that's very helpful. I am making the changes in a
> > forked
> > > > > repo, would I assign pull requests to you once I am finished?
> > > > >
> > > > > Boris Pelakh
> > > > > Ontologist, Developer, Software Architect
> > > > > boris.pelakh@semanticarts.com
> > > > > +1-321-243-3804
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > > > To: dev@rya.incubator.apache.org
> > > > > Subject: Re: Dataset not applied to queries
> > > > >
> > > > > Hi Boris,
> > > > > The execution of the query plan is done by the
> > > > ParallelEvaluationStrategy:
> > > > >
> > > > >
> > > >
> > >
> > https://github.com/apache/incubator-rya/blob/master/sail/src/main/java
> > /org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyIm
> > pl.java
> > > > >
> > > > > It looks like whoever did the rdf4j upgrade updated that class
> > > > > to
> > take
> > > > the
> > > > > dataset object in its constructor, but it doesn't seem to be
> > > > > used
> > > > anywhere
> > > > > in query evaluation.  That would be the class to modify,  but
> > > > > I'm
> > still
> > > > not
> > > > > clear on what the changes would look like since I'm not familiar
> > > > > with
> > > > what
> > > > > the contract is supposed to be.
> > > > >
> > > > >
> > > > >
> > > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > > > boris.pelakh@semanticarts.com
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > So, a
> > > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > > > is logically equivalent to
> > > > > >
> > > > > > SELECT ...
> > > > > > FROM <my-named-graph>
> > > > > > WHERE ...
> > > > > >
> > > > > > (overriding whatever FROM/FROM NAMED clauses actually
> > > > > > specified in
> > > the
> > > > > > query) I looked at
> > > > > >
> > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluate
> > > In
> > > > > > ternal(), and the dataset containing the overriding graph
> > > > > > names is passed in, but does not seem to be honored, i.e if I
> > > > > > have the following data:
> > > > > >
> > > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > > > >
> > > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> > > > > > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > > > > >
> > > > > > I am assuming that there is someplace where the TupleExpr
> > > > > > passed to evaluateInternal gets transformed into a scan
> > > > > > pattern for Accumulo, after the right index (spo/ops/pso) is
> > > > > > identified. If I remember correctly, S/P/O is used the the row
> > > > > > ID, and the graph is the
> > column
> > > > > > name (or family?). So the dataset should modify the scan
> > > > > > filter if
> > > > > applied correctly.
> > > > > >
> > > > > > Boris Pelakh
> > > > > > Ontologist, Developer, Software Architect
> > > > > > boris.pelakh@semanticarts.com
> > > > > > +1-321-243-3804
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > > > To: dev@rya.incubator.apache.org
> > > > > > Subject: Re: Dataset not applied to queries
> > > > > >
> > > > > > Hi Boris,
> > > > > > Unfortunately I'm not very familiar with that method -- can
> > > > > > you provide some more details into exactly what its supposed to
> do?
> > > > > > All of the connectors for implementing the sail api are in the
> > > > > > rya.sail, and the main classes to look at are
> > > > > > RdfCloudTripleStore, RyaSailRepository, and
> > > > > > RdfCloudTripleStoreConnection. All of these classes all extend
> > > > > > abstract implementations SAIL provides out of
> > the
> > > > > > box, so typically the way you extend them to do more stuff is
> > > > > > to
> > look
> > > > > > at the Sail implementation and customize it for Rya's data
> > > structures.
> > > > > > If you need any help or want to bounce any implementation
> > > > > > ideas off
> > > of
> > > > > > anyone, please send out an email over the dev list. Just let
> > > > > > us
> > know
> > > > > > how we can help!
> > > > > > Thanks,
> > > > > > Puja
> > > > > >
> > > > > >
> > > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > > > > <boris.pelakh@semanticarts.com
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > I am in the process of implementing a SPARQL 1.1-compliant
> > endpoint
> > > > > > > for web.rya so that Rya can be used as a federated
> > > > > > > repository
> > with
> > > > > > > RDF4J workbench.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > One of requirements is to be able to pass default-graph-uri
> > > > > > > and named-graph-uri filters external to the query to
> > > > > > > override the
> > graph
> > > > > > > filter in the query itself (see
> > > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > In the sail API this is accomplished by setting the dataset
> > > > > > > on
> > the
> > > > > > > query object (see
> > > > > > >
> > > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > > > but that setting does not seem to be honored by the Rya SAIL
> > > > > > > implementation. Any ideas on where I can start digging to
> > > > > > > correct
> > > > this?
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > (I have also tried wrapping the Rya repository connection in
> > > > > > > a ContextAwareConnection and setting readContexts, but the
> > > > > > > effect
> > is
> > > > > > > the same).
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > *Boris Pelakh*
> > > > > > >
> > > > > > > *Ontologist, Developer, Software Architect*
> > > > > > >
> > > > > > > *boris.pelakh@semanticarts.com
> > > > > > > <bo...@semanticarts.com>*
> > > > > > >
> > > > > > > *+1-321-243-3804*
> > > > > > >
> > > > > > > [image: SemanticArtsLogo]
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Dr. Adina Crainiceanu
> > > Associate Professor
> > > Computer Science Department
> > > United States Naval Academy
> > > 410-293-6822
> > > adina@usna.edu
> > > http://www.usna.edu/Users/cs/adina/
> > >
> >
> >
> > --
> > Dr. Adina Crainiceanu
> > Associate Professor
> > Computer Science Department
> > United States Naval Academy
> > 410-293-6822
> > adina@usna.edu
> > http://www.usna.edu/Users/cs/adina/
> >
>

RE: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Boris Pelakh <bo...@semanticarts.com>.

Hi, Jurgen

I looked at your source, and you do not appear to have addressed the default-graph-uri and named-graph-uri constraints defined in the SPARQL 1.1 protocol (https://www.w3.org/TR/sparql11-protocol/#protocol). Is this addressed somewhere other than SPARQLController.java?

Boris Pelakh
Ontologist, Developer, Software Architect
boris.pelakh@semanticarts.com
+1-321-243-3804


-----Original Message-----
From: Jürgen Jakobitsch <ju...@semantic-web.com> 
Sent: Wednesday, December 5, 2018 10:45 AM
To: dev@rya.incubator.apache.org
Subject: Re: SPARQL endpoint [Was: Dataset not applied to queries]

hi there, we've implemented the whole sparql endpoint anew.

some of the features from the old endpoint are still missing, but i think they need some re-engineering anyway, like send a user as a url paramter is not exactly a good idea..

i'm including a mail from i wrote from earlier this year (around april/may)

hi,

as mentioned in previous mails, we've setup a first draft of the proposed upgrade of rya's sparql endpoint.. again note, that we've setup a small debug/demo maven project using a sesame memory store to demonstrate the proposed changes. if the proposed upgrade of the sparql endpoint is welcome we would incorporate this with existing rya code to include all required rya features.
features:

1. full support for content-negotiation (essential within the linkeddata/semantic web realm) 2. SPARQL Service Description 3. more HTTP Status Codes (202 accepted, 400 bad request, 200 ok) 4. all RDF serialization formats available natively from sesame 5. customizable web endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
+ Styles)
6. valid XHTML for the endpoint
7. valid XHTML+RDFa in a browser for construct queries 8. a future rdf4j upgrade will not seriously affect the whole endpoint

the project is very easy to build and you can checkout all features on your local machine easily (examples are provided). the maven build will include a tomcat hosting this sample endpoint, descriptions and code can be found
here:

https://github.com/jj-semantic-web-com/rya-sparql-endpoint

any feedback, pointers, comments and wishes are highly welcome!

related JIRA task: https://issues.apache.org/jira/browse/RYA-477

kr jürgen





*Jürgen Jakobitsch*
Senior Technical Consultant
Semantic Web Company GmbH
EU: +43-14021235 <+43%201%204021235>
US: (415) 800-3776
Mobile: +43-676-6212710 <+43%20676%206212710> https://www.poolparty.biz https://www.semantic-web.com

*Download E-Book*: Introducing Semantic AI <https://www.poolparty.biz/machine-learning-meets-semantics/>


Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu <adina@usna.edu
>:

> Hi Jurgen,
>
> If you see this message, can you please reply?
>
> Boris, if you create a JIRA account you should be able to add comments 
> and "watch" the issue to be notified of changes.
>
> Adina
> On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh 
> <boris.pelakh@semanticarts.com
> >
> wrote:
>
> > Hi, Adina,
> >
> >
> > Thanks for the pointer, and I wish I had seen this prior to starting 
> > my effort. My work is essentially complete with the exception of the 
> > aforementioned defect in applying default and named graph filters, 
> > and it covers pretty much that entire Jira issue. I have no way of 
> > contacting Jurgen, as I only have read access to the JIRA instance 
> > you linked, but
> it
> > seems that no work has been done on that 'In Progress' issue for 
> > more
> than
> > 6 months.
> >
> >
> > Boris
> >
> > ________________________________
> > From: Adina Crainiceanu <ad...@usna.edu>
> > Sent: Wednesday, December 5, 2018 9:32:17 AM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: Dataset not applied to queries
> >
> > Hi Boris,
> >
> > There is some work currently being done on the SPARQL endpoint by 
> > Jurgen
> in
> > RYA-477 https://issues.apache.org/jira/browse/RYA-477
> > Let's make sure we discuss there ideas and design decisions on the 
> > dev list. I would hate if someone's work gets duplicated. In 
> > general, please check whether a JIRA issue for the bug/desired 
> > feature does not already exist 
> > https://issues.apache.org/jira/browse/RYA. If it does, collaborate 
> > with the person assigned to that issue (if any) or assign the issue 
> > to yourself (if none assigned). If not, create the issue and assign 
> > it to yourself. If you cannot assign an issue to yourself, send a 
> > message to
> the
> > dev list with the Jira username, so you can be added to the list of 
> > contributors in JIRA.
> >
> > Looking forward to your contributions!
> > Adina
> >
> >
> >
> > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com> wrote:
> >
> > > I can definitely take a look, but Aaron would also be a good 
> > > person if
> > its
> > > mostly using Accumulo backed Rya.  You're touching core Rya 
> > > classes so
> > the
> > > more eyes the better!
> > >
> > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh < 
> > > boris.pelakh@semanticarts.com>
> > > wrote:
> > >
> > > > Thanks, Puja, that's very helpful. I am making the changes in a
> forked
> > > > repo, would I assign pull requests to you once I am finished?
> > > >
> > > > Boris Pelakh
> > > > Ontologist, Developer, Software Architect 
> > > > boris.pelakh@semanticarts.com
> > > > +1-321-243-3804
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Puja Valiyil <pu...@gmail.com>
> > > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > > To: dev@rya.incubator.apache.org
> > > > Subject: Re: Dataset not applied to queries
> > > >
> > > > Hi Boris,
> > > > The execution of the query plan is done by the
> > > ParallelEvaluationStrategy:
> > > >
> > > >
> > >
> >
> https://github.com/apache/incubator-rya/blob/master/sail/src/main/java
> /org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyIm
> pl.java
> > > >
> > > > It looks like whoever did the rdf4j upgrade updated that class 
> > > > to
> take
> > > the
> > > > dataset object in its constructor, but it doesn't seem to be 
> > > > used
> > > anywhere
> > > > in query evaluation.  That would be the class to modify,  but 
> > > > I'm
> still
> > > not
> > > > clear on what the changes would look like since I'm not familiar 
> > > > with
> > > what
> > > > the contract is supposed to be.
> > > >
> > > >
> > > >
> > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > > boris.pelakh@semanticarts.com
> > > > >
> > > > wrote:
> > > >
> > > > > So, a
> > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > > is logically equivalent to
> > > > >
> > > > > SELECT ...
> > > > > FROM <my-named-graph>
> > > > > WHERE ...
> > > > >
> > > > > (overriding whatever FROM/FROM NAMED clauses actually 
> > > > > specified in
> > the
> > > > > query) I looked at
> > > > >
> > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluate
> > In
> > > > > ternal(), and the dataset containing the overriding graph 
> > > > > names is passed in, but does not seem to be honored, i.e if I 
> > > > > have the following data:
> > > > >
> > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > > >
> > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with 
> > > > > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > > > >
> > > > > I am assuming that there is someplace where the TupleExpr 
> > > > > passed to evaluateInternal gets transformed into a scan 
> > > > > pattern for Accumulo, after the right index (spo/ops/pso) is 
> > > > > identified. If I remember correctly, S/P/O is used the the row 
> > > > > ID, and the graph is the
> column
> > > > > name (or family?). So the dataset should modify the scan 
> > > > > filter if
> > > > applied correctly.
> > > > >
> > > > > Boris Pelakh
> > > > > Ontologist, Developer, Software Architect 
> > > > > boris.pelakh@semanticarts.com
> > > > > +1-321-243-3804
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > > To: dev@rya.incubator.apache.org
> > > > > Subject: Re: Dataset not applied to queries
> > > > >
> > > > > Hi Boris,
> > > > > Unfortunately I'm not very familiar with that method -- can 
> > > > > you provide some more details into exactly what its supposed to do?
> > > > > All of the connectors for implementing the sail api are in the 
> > > > > rya.sail, and the main classes to look at are 
> > > > > RdfCloudTripleStore, RyaSailRepository, and 
> > > > > RdfCloudTripleStoreConnection. All of these classes all extend 
> > > > > abstract implementations SAIL provides out of
> the
> > > > > box, so typically the way you extend them to do more stuff is 
> > > > > to
> look
> > > > > at the Sail implementation and customize it for Rya's data
> > structures.
> > > > > If you need any help or want to bounce any implementation 
> > > > > ideas off
> > of
> > > > > anyone, please send out an email over the dev list. Just let 
> > > > > us
> know
> > > > > how we can help!
> > > > > Thanks,
> > > > > Puja
> > > > >
> > > > >
> > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh 
> > > > > <boris.pelakh@semanticarts.com
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > I am in the process of implementing a SPARQL 1.1-compliant
> endpoint
> > > > > > for web.rya so that Rya can be used as a federated 
> > > > > > repository
> with
> > > > > > RDF4J workbench.
> > > > > >
> > > > > >
> > > > > >
> > > > > > One of requirements is to be able to pass default-graph-uri 
> > > > > > and named-graph-uri filters external to the query to 
> > > > > > override the
> graph
> > > > > > filter in the query itself (see 
> > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > > >
> > > > > >
> > > > > >
> > > > > > In the sail API this is accomplished by setting the dataset 
> > > > > > on
> the
> > > > > > query object (see
> > > > > >
> > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > > but that setting does not seem to be honored by the Rya SAIL 
> > > > > > implementation. Any ideas on where I can start digging to 
> > > > > > correct
> > > this?
> > > > > >
> > > > > >
> > > > > >
> > > > > > (I have also tried wrapping the Rya repository connection in 
> > > > > > a ContextAwareConnection and setting readContexts, but the 
> > > > > > effect
> is
> > > > > > the same).
> > > > > >
> > > > > >
> > > > > >
> > > > > > *Boris Pelakh*
> > > > > >
> > > > > > *Ontologist, Developer, Software Architect*
> > > > > >
> > > > > > *boris.pelakh@semanticarts.com 
> > > > > > <bo...@semanticarts.com>*
> > > > > >
> > > > > > *+1-321-243-3804*
> > > > > >
> > > > > > [image: SemanticArtsLogo]
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> >
> > --
> > Dr. Adina Crainiceanu
> > Associate Professor
> > Computer Science Department
> > United States Naval Academy
> > 410-293-6822
> > adina@usna.edu
> > http://www.usna.edu/Users/cs/adina/
> >
>
>
> --
> Dr. Adina Crainiceanu
> Associate Professor
> Computer Science Department
> United States Naval Academy
> 410-293-6822
> adina@usna.edu
> http://www.usna.edu/Users/cs/adina/
>

Re: SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Jürgen Jakobitsch <ju...@semantic-web.com>.

hi there, we've implemented the whole sparql endpoint anew.

some of the features from the old endpoint are still missing, but i think
they need some re-engineering anyway, like send a user
as a url paramter is not exactly a good idea..

i'm including a mail from i wrote from earlier this year (around april/may)

hi,

as mentioned in previous mails, we've setup a first draft of the proposed
upgrade of rya's sparql endpoint.. again note, that we've setup a small
debug/demo maven project using a sesame memory store to demonstrate the
proposed changes. if the proposed upgrade of the sparql endpoint is welcome
we would incorporate this with existing rya code to include all required rya
features.
features:

1. full support for content-negotiation (essential within the
linkeddata/semantic web realm)
2. SPARQL Service Description
3. more HTTP Status Codes (202 accepted, 400 bad request, 200 ok)
4. all RDF serialization formats available natively from sesame
5. customizable web endpoint (via a sesame MAVWriter (ModelAndView) + JSPs
+ Styles)
6. valid XHTML for the endpoint
7. valid XHTML+RDFa in a browser for construct queries
8. a future rdf4j upgrade will not seriously affect the whole endpoint

the project is very easy to build and you can checkout all features on your
local machine easily (examples are provided). the maven build will include
a tomcat hosting this sample endpoint, descriptions and code can be found
here:

https://github.com/jj-semantic-web-com/rya-sparql-endpoint

any feedback, pointers, comments and wishes are highly welcome!

related JIRA task: https://issues.apache.org/jira/browse/RYA-477

kr jürgen





*Jürgen Jakobitsch*
Senior Technical Consultant
Semantic Web Company GmbH
EU: +43-14021235 <+43%201%204021235>
US: (415) 800-3776
Mobile: +43-676-6212710 <+43%20676%206212710>
https://www.poolparty.biz
https://www.semantic-web.com

*Download E-Book*: Introducing Semantic AI
<https://www.poolparty.biz/machine-learning-meets-semantics/>


Am Mi., 5. Dez. 2018 um 16:28 Uhr schrieb Adina Crainiceanu <adina@usna.edu
>:

> Hi Jurgen,
>
> If you see this message, can you please reply?
>
> Boris, if you create a JIRA account you should be able to add comments and
> "watch" the issue to be notified of changes.
>
> Adina
> On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh <boris.pelakh@semanticarts.com
> >
> wrote:
>
> > Hi, Adina,
> >
> >
> > Thanks for the pointer, and I wish I had seen this prior to starting my
> > effort. My work is essentially complete with the exception of the
> > aforementioned defect in applying default and named graph filters, and it
> > covers pretty much that entire Jira issue. I have no way of contacting
> > Jurgen, as I only have read access to the JIRA instance you linked, but
> it
> > seems that no work has been done on that 'In Progress' issue for more
> than
> > 6 months.
> >
> >
> > Boris
> >
> > ________________________________
> > From: Adina Crainiceanu <ad...@usna.edu>
> > Sent: Wednesday, December 5, 2018 9:32:17 AM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: Dataset not applied to queries
> >
> > Hi Boris,
> >
> > There is some work currently being done on the SPARQL endpoint by Jurgen
> in
> > RYA-477 https://issues.apache.org/jira/browse/RYA-477
> > Let's make sure we discuss there ideas and design decisions on the dev
> > list. I would hate if someone's work gets duplicated. In general, please
> > check whether a JIRA issue for the bug/desired feature does not already
> > exist https://issues.apache.org/jira/browse/RYA. If it does, collaborate
> > with the person assigned to that issue (if any) or assign the issue to
> > yourself (if none assigned). If not, create the issue and assign it to
> > yourself. If you cannot assign an issue to yourself, send a message to
> the
> > dev list with the Jira username, so you can be added to the list of
> > contributors in JIRA.
> >
> > Looking forward to your contributions!
> > Adina
> >
> >
> >
> > On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com> wrote:
> >
> > > I can definitely take a look, but Aaron would also be a good person if
> > its
> > > mostly using Accumulo backed Rya.  You're touching core Rya classes so
> > the
> > > more eyes the better!
> > >
> > > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> > > boris.pelakh@semanticarts.com>
> > > wrote:
> > >
> > > > Thanks, Puja, that's very helpful. I am making the changes in a
> forked
> > > > repo, would I assign pull requests to you once I am finished?
> > > >
> > > > Boris Pelakh
> > > > Ontologist, Developer, Software Architect
> > > > boris.pelakh@semanticarts.com
> > > > +1-321-243-3804
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Puja Valiyil <pu...@gmail.com>
> > > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > > To: dev@rya.incubator.apache.org
> > > > Subject: Re: Dataset not applied to queries
> > > >
> > > > Hi Boris,
> > > > The execution of the query plan is done by the
> > > ParallelEvaluationStrategy:
> > > >
> > > >
> > >
> >
> https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
> > > >
> > > > It looks like whoever did the rdf4j upgrade updated that class to
> take
> > > the
> > > > dataset object in its constructor, but it doesn't seem to be used
> > > anywhere
> > > > in query evaluation.  That would be the class to modify,  but I'm
> still
> > > not
> > > > clear on what the changes would look like since I'm not familiar with
> > > what
> > > > the contract is supposed to be.
> > > >
> > > >
> > > >
> > > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > > boris.pelakh@semanticarts.com
> > > > >
> > > > wrote:
> > > >
> > > > > So, a
> > /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > > is logically equivalent to
> > > > >
> > > > > SELECT ...
> > > > > FROM <my-named-graph>
> > > > > WHERE ...
> > > > >
> > > > > (overriding whatever FROM/FROM NAMED clauses actually specified in
> > the
> > > > > query) I looked at
> > > > >
> > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateIn
> > > > > ternal(), and the dataset containing the overriding graph names is
> > > > > passed in, but does not seem to be honored, i.e if I have the
> > > > > following data:
> > > > >
> > > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > > >
> > > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> > > > > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > > > >
> > > > > I am assuming that there is someplace where the TupleExpr passed to
> > > > > evaluateInternal gets transformed into a scan pattern for Accumulo,
> > > > > after the right index (spo/ops/pso) is identified. If I remember
> > > > > correctly, S/P/O is used the the row ID, and the graph is the
> column
> > > > > name (or family?). So the dataset should modify the scan filter if
> > > > applied correctly.
> > > > >
> > > > > Boris Pelakh
> > > > > Ontologist, Developer, Software Architect
> > > > > boris.pelakh@semanticarts.com
> > > > > +1-321-243-3804
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: Puja Valiyil <pu...@gmail.com>
> > > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > > To: dev@rya.incubator.apache.org
> > > > > Subject: Re: Dataset not applied to queries
> > > > >
> > > > > Hi Boris,
> > > > > Unfortunately I'm not very familiar with that method -- can you
> > > > > provide some more details into exactly what its supposed to do?
> > > > > All of the connectors for implementing the sail api are in the
> > > > > rya.sail, and the main classes to look at are RdfCloudTripleStore,
> > > > > RyaSailRepository, and RdfCloudTripleStoreConnection. All of these
> > > > > classes all extend abstract implementations SAIL provides out of
> the
> > > > > box, so typically the way you extend them to do more stuff is to
> look
> > > > > at the Sail implementation and customize it for Rya's data
> > structures.
> > > > > If you need any help or want to bounce any implementation ideas off
> > of
> > > > > anyone, please send out an email over the dev list. Just let us
> know
> > > > > how we can help!
> > > > > Thanks,
> > > > > Puja
> > > > >
> > > > >
> > > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > > > <boris.pelakh@semanticarts.com
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > I am in the process of implementing a SPARQL 1.1-compliant
> endpoint
> > > > > > for web.rya so that Rya can be used as a federated repository
> with
> > > > > > RDF4J workbench.
> > > > > >
> > > > > >
> > > > > >
> > > > > > One of requirements is to be able to pass default-graph-uri and
> > > > > > named-graph-uri filters external to the query to override the
> graph
> > > > > > filter in the query itself (see
> > > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > > >
> > > > > >
> > > > > >
> > > > > > In the sail API this is accomplished by setting the dataset on
> the
> > > > > > query object (see
> > > > > >
> > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > > but that setting does not seem to be honored by the Rya SAIL
> > > > > > implementation. Any ideas on where I can start digging to correct
> > > this?
> > > > > >
> > > > > >
> > > > > >
> > > > > > (I have also tried wrapping the Rya repository connection in a
> > > > > > ContextAwareConnection and setting readContexts, but the effect
> is
> > > > > > the same).
> > > > > >
> > > > > >
> > > > > >
> > > > > > *Boris Pelakh*
> > > > > >
> > > > > > *Ontologist, Developer, Software Architect*
> > > > > >
> > > > > > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> > > > > >
> > > > > > *+1-321-243-3804*
> > > > > >
> > > > > > [image: SemanticArtsLogo]
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> >
> > --
> > Dr. Adina Crainiceanu
> > Associate Professor
> > Computer Science Department
> > United States Naval Academy
> > 410-293-6822
> > adina@usna.edu
> > http://www.usna.edu/Users/cs/adina/
> >
>
>
> --
> Dr. Adina Crainiceanu
> Associate Professor
> Computer Science Department
> United States Naval Academy
> 410-293-6822
> adina@usna.edu
> http://www.usna.edu/Users/cs/adina/
>

SPARQL endpoint [Was: Dataset not applied to queries]

Posted by Adina Crainiceanu <ad...@usna.edu>.

Hi Jurgen,

If you see this message, can you please reply?

Boris, if you create a JIRA account you should be able to add comments and
"watch" the issue to be notified of changes.

Adina
On Wed, Dec 5, 2018 at 9:41 AM Boris Pelakh <bo...@semanticarts.com>
wrote:

> Hi, Adina,
>
>
> Thanks for the pointer, and I wish I had seen this prior to starting my
> effort. My work is essentially complete with the exception of the
> aforementioned defect in applying default and named graph filters, and it
> covers pretty much that entire Jira issue. I have no way of contacting
> Jurgen, as I only have read access to the JIRA instance you linked, but it
> seems that no work has been done on that 'In Progress' issue for more than
> 6 months.
>
>
> Boris
>
> ________________________________
> From: Adina Crainiceanu <ad...@usna.edu>
> Sent: Wednesday, December 5, 2018 9:32:17 AM
> To: dev@rya.incubator.apache.org
> Subject: Re: Dataset not applied to queries
>
> Hi Boris,
>
> There is some work currently being done on the SPARQL endpoint by Jurgen in
> RYA-477 https://issues.apache.org/jira/browse/RYA-477
> Let's make sure we discuss there ideas and design decisions on the dev
> list. I would hate if someone's work gets duplicated. In general, please
> check whether a JIRA issue for the bug/desired feature does not already
> exist https://issues.apache.org/jira/browse/RYA. If it does, collaborate
> with the person assigned to that issue (if any) or assign the issue to
> yourself (if none assigned). If not, create the issue and assign it to
> yourself. If you cannot assign an issue to yourself, send a message to the
> dev list with the Jira username, so you can be added to the list of
> contributors in JIRA.
>
> Looking forward to your contributions!
> Adina
>
>
>
> On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com> wrote:
>
> > I can definitely take a look, but Aaron would also be a good person if
> its
> > mostly using Accumulo backed Rya.  You're touching core Rya classes so
> the
> > more eyes the better!
> >
> > On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> > boris.pelakh@semanticarts.com>
> > wrote:
> >
> > > Thanks, Puja, that's very helpful. I am making the changes in a forked
> > > repo, would I assign pull requests to you once I am finished?
> > >
> > > Boris Pelakh
> > > Ontologist, Developer, Software Architect
> > > boris.pelakh@semanticarts.com
> > > +1-321-243-3804
> > >
> > >
> > > -----Original Message-----
> > > From: Puja Valiyil <pu...@gmail.com>
> > > Sent: Tuesday, December 4, 2018 10:12 AM
> > > To: dev@rya.incubator.apache.org
> > > Subject: Re: Dataset not applied to queries
> > >
> > > Hi Boris,
> > > The execution of the query plan is done by the
> > ParallelEvaluationStrategy:
> > >
> > >
> >
> https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
> > >
> > > It looks like whoever did the rdf4j upgrade updated that class to take
> > the
> > > dataset object in its constructor, but it doesn't seem to be used
> > anywhere
> > > in query evaluation.  That would be the class to modify,  but I'm still
> > not
> > > clear on what the changes would look like since I'm not familiar with
> > what
> > > the contract is supposed to be.
> > >
> > >
> > >
> > > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> > boris.pelakh@semanticarts.com
> > > >
> > > wrote:
> > >
> > > > So, a
> /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > > is logically equivalent to
> > > >
> > > > SELECT ...
> > > > FROM <my-named-graph>
> > > > WHERE ...
> > > >
> > > > (overriding whatever FROM/FROM NAMED clauses actually specified in
> the
> > > > query) I looked at
> > > >
> org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateIn
> > > > ternal(), and the dataset containing the overriding graph names is
> > > > passed in, but does not seem to be honored, i.e if I have the
> > > > following data:
> > > >
> > > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > > >
> > > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> > > > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > > >
> > > > I am assuming that there is someplace where the TupleExpr passed to
> > > > evaluateInternal gets transformed into a scan pattern for Accumulo,
> > > > after the right index (spo/ops/pso) is identified. If I remember
> > > > correctly, S/P/O is used the the row ID, and the graph is the column
> > > > name (or family?). So the dataset should modify the scan filter if
> > > applied correctly.
> > > >
> > > > Boris Pelakh
> > > > Ontologist, Developer, Software Architect
> > > > boris.pelakh@semanticarts.com
> > > > +1-321-243-3804
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Puja Valiyil <pu...@gmail.com>
> > > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > > To: dev@rya.incubator.apache.org
> > > > Subject: Re: Dataset not applied to queries
> > > >
> > > > Hi Boris,
> > > > Unfortunately I'm not very familiar with that method -- can you
> > > > provide some more details into exactly what its supposed to do?
> > > > All of the connectors for implementing the sail api are in the
> > > > rya.sail, and the main classes to look at are RdfCloudTripleStore,
> > > > RyaSailRepository, and RdfCloudTripleStoreConnection. All of these
> > > > classes all extend abstract implementations SAIL provides out of the
> > > > box, so typically the way you extend them to do more stuff is to look
> > > > at the Sail implementation and customize it for Rya's data
> structures.
> > > > If you need any help or want to bounce any implementation ideas off
> of
> > > > anyone, please send out an email over the dev list. Just let us know
> > > > how we can help!
> > > > Thanks,
> > > > Puja
> > > >
> > > >
> > > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > > <boris.pelakh@semanticarts.com
> > > > >
> > > > wrote:
> > > >
> > > > > I am in the process of implementing a SPARQL 1.1-compliant endpoint
> > > > > for web.rya so that Rya can be used as a federated repository with
> > > > > RDF4J workbench.
> > > > >
> > > > >
> > > > >
> > > > > One of requirements is to be able to pass default-graph-uri and
> > > > > named-graph-uri filters external to the query to override the graph
> > > > > filter in the query itself (see
> > > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > > >
> > > > >
> > > > >
> > > > > In the sail API this is accomplished by setting the dataset on the
> > > > > query object (see
> > > > >
> http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > > but that setting does not seem to be honored by the Rya SAIL
> > > > > implementation. Any ideas on where I can start digging to correct
> > this?
> > > > >
> > > > >
> > > > >
> > > > > (I have also tried wrapping the Rya repository connection in a
> > > > > ContextAwareConnection and setting readContexts, but the effect is
> > > > > the same).
> > > > >
> > > > >
> > > > >
> > > > > *Boris Pelakh*
> > > > >
> > > > > *Ontologist, Developer, Software Architect*
> > > > >
> > > > > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> > > > >
> > > > > *+1-321-243-3804*
> > > > >
> > > > > [image: SemanticArtsLogo]
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
>
>
> --
> Dr. Adina Crainiceanu
> Associate Professor
> Computer Science Department
> United States Naval Academy
> 410-293-6822
> adina@usna.edu
> http://www.usna.edu/Users/cs/adina/
>


-- 
Dr. Adina Crainiceanu
Associate Professor
Computer Science Department
United States Naval Academy
410-293-6822
adina@usna.edu
http://www.usna.edu/Users/cs/adina/

Re: Dataset not applied to queries

Posted by Boris Pelakh <bo...@semanticarts.com>.

Hi, Adina,


Thanks for the pointer, and I wish I had seen this prior to starting my effort. My work is essentially complete with the exception of the aforementioned defect in applying default and named graph filters, and it covers pretty much that entire Jira issue. I have no way of contacting Jurgen, as I only have read access to the JIRA instance you linked, but it seems that no work has been done on that 'In Progress' issue for more than 6 months.


Boris

________________________________
From: Adina Crainiceanu <ad...@usna.edu>
Sent: Wednesday, December 5, 2018 9:32:17 AM
To: dev@rya.incubator.apache.org
Subject: Re: Dataset not applied to queries

Hi Boris,

There is some work currently being done on the SPARQL endpoint by Jurgen in
RYA-477 https://issues.apache.org/jira/browse/RYA-477
Let's make sure we discuss there ideas and design decisions on the dev
list. I would hate if someone's work gets duplicated. In general, please
check whether a JIRA issue for the bug/desired feature does not already
exist https://issues.apache.org/jira/browse/RYA. If it does, collaborate
with the person assigned to that issue (if any) or assign the issue to
yourself (if none assigned). If not, create the issue and assign it to
yourself. If you cannot assign an issue to yourself, send a message to the
dev list with the Jira username, so you can be added to the list of
contributors in JIRA.

Looking forward to your contributions!
Adina



On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com> wrote:

> I can definitely take a look, but Aaron would also be a good person if its
> mostly using Accumulo backed Rya.  You're touching core Rya classes so the
> more eyes the better!
>
> On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> boris.pelakh@semanticarts.com>
> wrote:
>
> > Thanks, Puja, that's very helpful. I am making the changes in a forked
> > repo, would I assign pull requests to you once I am finished?
> >
> > Boris Pelakh
> > Ontologist, Developer, Software Architect
> > boris.pelakh@semanticarts.com
> > +1-321-243-3804
> >
> >
> > -----Original Message-----
> > From: Puja Valiyil <pu...@gmail.com>
> > Sent: Tuesday, December 4, 2018 10:12 AM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: Dataset not applied to queries
> >
> > Hi Boris,
> > The execution of the query plan is done by the
> ParallelEvaluationStrategy:
> >
> >
> https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
> >
> > It looks like whoever did the rdf4j upgrade updated that class to take
> the
> > dataset object in its constructor, but it doesn't seem to be used
> anywhere
> > in query evaluation.  That would be the class to modify,  but I'm still
> not
> > clear on what the changes would look like since I'm not familiar with
> what
> > the contract is supposed to be.
> >
> >
> >
> > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> boris.pelakh@semanticarts.com
> > >
> > wrote:
> >
> > > So, a /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > is logically equivalent to
> > >
> > > SELECT ...
> > > FROM <my-named-graph>
> > > WHERE ...
> > >
> > > (overriding whatever FROM/FROM NAMED clauses actually specified in the
> > > query) I looked at
> > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateIn
> > > ternal(), and the dataset containing the overriding graph names is
> > > passed in, but does not seem to be honored, i.e if I have the
> > > following data:
> > >
> > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > >
> > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> > > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > >
> > > I am assuming that there is someplace where the TupleExpr passed to
> > > evaluateInternal gets transformed into a scan pattern for Accumulo,
> > > after the right index (spo/ops/pso) is identified. If I remember
> > > correctly, S/P/O is used the the row ID, and the graph is the column
> > > name (or family?). So the dataset should modify the scan filter if
> > applied correctly.
> > >
> > > Boris Pelakh
> > > Ontologist, Developer, Software Architect
> > > boris.pelakh@semanticarts.com
> > > +1-321-243-3804
> > >
> > >
> > > -----Original Message-----
> > > From: Puja Valiyil <pu...@gmail.com>
> > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > To: dev@rya.incubator.apache.org
> > > Subject: Re: Dataset not applied to queries
> > >
> > > Hi Boris,
> > > Unfortunately I'm not very familiar with that method -- can you
> > > provide some more details into exactly what its supposed to do?
> > > All of the connectors for implementing the sail api are in the
> > > rya.sail, and the main classes to look at are RdfCloudTripleStore,
> > > RyaSailRepository, and RdfCloudTripleStoreConnection. All of these
> > > classes all extend abstract implementations SAIL provides out of the
> > > box, so typically the way you extend them to do more stuff is to look
> > > at the Sail implementation and customize it for Rya's data structures.
> > > If you need any help or want to bounce any implementation ideas off of
> > > anyone, please send out an email over the dev list. Just let us know
> > > how we can help!
> > > Thanks,
> > > Puja
> > >
> > >
> > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > <boris.pelakh@semanticarts.com
> > > >
> > > wrote:
> > >
> > > > I am in the process of implementing a SPARQL 1.1-compliant endpoint
> > > > for web.rya so that Rya can be used as a federated repository with
> > > > RDF4J workbench.
> > > >
> > > >
> > > >
> > > > One of requirements is to be able to pass default-graph-uri and
> > > > named-graph-uri filters external to the query to override the graph
> > > > filter in the query itself (see
> > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > >
> > > >
> > > >
> > > > In the sail API this is accomplished by setting the dataset on the
> > > > query object (see
> > > > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > but that setting does not seem to be honored by the Rya SAIL
> > > > implementation. Any ideas on where I can start digging to correct
> this?
> > > >
> > > >
> > > >
> > > > (I have also tried wrapping the Rya repository connection in a
> > > > ContextAwareConnection and setting readContexts, but the effect is
> > > > the same).
> > > >
> > > >
> > > >
> > > > *Boris Pelakh*
> > > >
> > > > *Ontologist, Developer, Software Architect*
> > > >
> > > > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> > > >
> > > > *+1-321-243-3804*
> > > >
> > > > [image: SemanticArtsLogo]
> > > >
> > > >
> > > >
> > >
> >
>


--
Dr. Adina Crainiceanu
Associate Professor
Computer Science Department
United States Naval Academy
410-293-6822
adina@usna.edu
http://www.usna.edu/Users/cs/adina/

Re: Dataset not applied to queries

Posted by Adina Crainiceanu <ad...@usna.edu>.

Hi Boris,

There is some work currently being done on the SPARQL endpoint by Jurgen in
RYA-477 https://issues.apache.org/jira/browse/RYA-477
Let's make sure we discuss there ideas and design decisions on the dev
list. I would hate if someone's work gets duplicated. In general, please
check whether a JIRA issue for the bug/desired feature does not already
exist https://issues.apache.org/jira/browse/RYA. If it does, collaborate
with the person assigned to that issue (if any) or assign the issue to
yourself (if none assigned). If not, create the issue and assign it to
yourself. If you cannot assign an issue to yourself, send a message to the
dev list with the Jira username, so you can be added to the list of
contributors in JIRA.

Looking forward to your contributions!
Adina



On Tue, Dec 4, 2018 at 11:16 AM Puja Valiyil <pu...@gmail.com> wrote:

> I can definitely take a look, but Aaron would also be a good person if its
> mostly using Accumulo backed Rya.  You're touching core Rya classes so the
> more eyes the better!
>
> On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <
> boris.pelakh@semanticarts.com>
> wrote:
>
> > Thanks, Puja, that's very helpful. I am making the changes in a forked
> > repo, would I assign pull requests to you once I am finished?
> >
> > Boris Pelakh
> > Ontologist, Developer, Software Architect
> > boris.pelakh@semanticarts.com
> > +1-321-243-3804
> >
> >
> > -----Original Message-----
> > From: Puja Valiyil <pu...@gmail.com>
> > Sent: Tuesday, December 4, 2018 10:12 AM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: Dataset not applied to queries
> >
> > Hi Boris,
> > The execution of the query plan is done by the
> ParallelEvaluationStrategy:
> >
> >
> https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
> >
> > It looks like whoever did the rdf4j upgrade updated that class to take
> the
> > dataset object in its constructor, but it doesn't seem to be used
> anywhere
> > in query evaluation.  That would be the class to modify,  but I'm still
> not
> > clear on what the changes would look like since I'm not familiar with
> what
> > the contract is supposed to be.
> >
> >
> >
> > On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <
> boris.pelakh@semanticarts.com
> > >
> > wrote:
> >
> > > So, a /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > > is logically equivalent to
> > >
> > > SELECT ...
> > > FROM <my-named-graph>
> > > WHERE ...
> > >
> > > (overriding whatever FROM/FROM NAMED clauses actually specified in the
> > > query) I looked at
> > > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateIn
> > > ternal(), and the dataset containing the overriding graph names is
> > > passed in, but does not seem to be honored, i.e if I have the
> > > following data:
> > >
> > > ns:g1 { ns:p1 ns:pred ns:o1 }
> > > ns:g2 { ns:p2 ns:pred ns:o2 }
> > >
> > > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> > > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> > >
> > > I am assuming that there is someplace where the TupleExpr passed to
> > > evaluateInternal gets transformed into a scan pattern for Accumulo,
> > > after the right index (spo/ops/pso) is identified. If I remember
> > > correctly, S/P/O is used the the row ID, and the graph is the column
> > > name (or family?). So the dataset should modify the scan filter if
> > applied correctly.
> > >
> > > Boris Pelakh
> > > Ontologist, Developer, Software Architect
> > > boris.pelakh@semanticarts.com
> > > +1-321-243-3804
> > >
> > >
> > > -----Original Message-----
> > > From: Puja Valiyil <pu...@gmail.com>
> > > Sent: Tuesday, December 4, 2018 9:31 AM
> > > To: dev@rya.incubator.apache.org
> > > Subject: Re: Dataset not applied to queries
> > >
> > > Hi Boris,
> > > Unfortunately I'm not very familiar with that method -- can you
> > > provide some more details into exactly what its supposed to do?
> > > All of the connectors for implementing the sail api are in the
> > > rya.sail, and the main classes to look at are RdfCloudTripleStore,
> > > RyaSailRepository, and RdfCloudTripleStoreConnection. All of these
> > > classes all extend abstract implementations SAIL provides out of the
> > > box, so typically the way you extend them to do more stuff is to look
> > > at the Sail implementation and customize it for Rya's data structures.
> > > If you need any help or want to bounce any implementation ideas off of
> > > anyone, please send out an email over the dev list. Just let us know
> > > how we can help!
> > > Thanks,
> > > Puja
> > >
> > >
> > > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > > <boris.pelakh@semanticarts.com
> > > >
> > > wrote:
> > >
> > > > I am in the process of implementing a SPARQL 1.1-compliant endpoint
> > > > for web.rya so that Rya can be used as a federated repository with
> > > > RDF4J workbench.
> > > >
> > > >
> > > >
> > > > One of requirements is to be able to pass default-graph-uri and
> > > > named-graph-uri filters external to the query to override the graph
> > > > filter in the query itself (see
> > > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > > >
> > > >
> > > >
> > > > In the sail API this is accomplished by setting the dataset on the
> > > > query object (see
> > > > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > > but that setting does not seem to be honored by the Rya SAIL
> > > > implementation. Any ideas on where I can start digging to correct
> this?
> > > >
> > > >
> > > >
> > > > (I have also tried wrapping the Rya repository connection in a
> > > > ContextAwareConnection and setting readContexts, but the effect is
> > > > the same).
> > > >
> > > >
> > > >
> > > > *Boris Pelakh*
> > > >
> > > > *Ontologist, Developer, Software Architect*
> > > >
> > > > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> > > >
> > > > *+1-321-243-3804*
> > > >
> > > > [image: SemanticArtsLogo]
> > > >
> > > >
> > > >
> > >
> >
>


-- 
Dr. Adina Crainiceanu
Associate Professor
Computer Science Department
United States Naval Academy
410-293-6822
adina@usna.edu
http://www.usna.edu/Users/cs/adina/

Re: Dataset not applied to queries

Posted by Puja Valiyil <pu...@gmail.com>.

I can definitely take a look, but Aaron would also be a good person if its
mostly using Accumulo backed Rya.  You're touching core Rya classes so the
more eyes the better!

On Tue, Dec 4, 2018 at 10:14 AM Boris Pelakh <bo...@semanticarts.com>
wrote:

> Thanks, Puja, that's very helpful. I am making the changes in a forked
> repo, would I assign pull requests to you once I am finished?
>
> Boris Pelakh
> Ontologist, Developer, Software Architect
> boris.pelakh@semanticarts.com
> +1-321-243-3804
>
>
> -----Original Message-----
> From: Puja Valiyil <pu...@gmail.com>
> Sent: Tuesday, December 4, 2018 10:12 AM
> To: dev@rya.incubator.apache.org
> Subject: Re: Dataset not applied to queries
>
> Hi Boris,
> The execution of the query plan is done by the ParallelEvaluationStrategy:
>
> https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
>
> It looks like whoever did the rdf4j upgrade updated that class to take the
> dataset object in its constructor, but it doesn't seem to be used anywhere
> in query evaluation.  That would be the class to modify,  but I'm still not
> clear on what the changes would look like since I'm not familiar with what
> the contract is supposed to be.
>
>
>
> On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <boris.pelakh@semanticarts.com
> >
> wrote:
>
> > So, a /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph
> > is logically equivalent to
> >
> > SELECT ...
> > FROM <my-named-graph>
> > WHERE ...
> >
> > (overriding whatever FROM/FROM NAMED clauses actually specified in the
> > query) I looked at
> > org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateIn
> > ternal(), and the dataset containing the overriding graph names is
> > passed in, but does not seem to be honored, i.e if I have the
> > following data:
> >
> > ns:g1 { ns:p1 ns:pred ns:o1 }
> > ns:g2 { ns:p2 ns:pred ns:o2 }
> >
> > and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> > default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
> >
> > I am assuming that there is someplace where the TupleExpr passed to
> > evaluateInternal gets transformed into a scan pattern for Accumulo,
> > after the right index (spo/ops/pso) is identified. If I remember
> > correctly, S/P/O is used the the row ID, and the graph is the column
> > name (or family?). So the dataset should modify the scan filter if
> applied correctly.
> >
> > Boris Pelakh
> > Ontologist, Developer, Software Architect
> > boris.pelakh@semanticarts.com
> > +1-321-243-3804
> >
> >
> > -----Original Message-----
> > From: Puja Valiyil <pu...@gmail.com>
> > Sent: Tuesday, December 4, 2018 9:31 AM
> > To: dev@rya.incubator.apache.org
> > Subject: Re: Dataset not applied to queries
> >
> > Hi Boris,
> > Unfortunately I'm not very familiar with that method -- can you
> > provide some more details into exactly what its supposed to do?
> > All of the connectors for implementing the sail api are in the
> > rya.sail, and the main classes to look at are RdfCloudTripleStore,
> > RyaSailRepository, and RdfCloudTripleStoreConnection. All of these
> > classes all extend abstract implementations SAIL provides out of the
> > box, so typically the way you extend them to do more stuff is to look
> > at the Sail implementation and customize it for Rya's data structures.
> > If you need any help or want to bounce any implementation ideas off of
> > anyone, please send out an email over the dev list. Just let us know
> > how we can help!
> > Thanks,
> > Puja
> >
> >
> > On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh
> > <boris.pelakh@semanticarts.com
> > >
> > wrote:
> >
> > > I am in the process of implementing a SPARQL 1.1-compliant endpoint
> > > for web.rya so that Rya can be used as a federated repository with
> > > RDF4J workbench.
> > >
> > >
> > >
> > > One of requirements is to be able to pass default-graph-uri and
> > > named-graph-uri filters external to the query to override the graph
> > > filter in the query itself (see
> > > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> > >
> > >
> > >
> > > In the sail API this is accomplished by setting the dataset on the
> > > query object (see
> > > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > > but that setting does not seem to be honored by the Rya SAIL
> > > implementation. Any ideas on where I can start digging to correct this?
> > >
> > >
> > >
> > > (I have also tried wrapping the Rya repository connection in a
> > > ContextAwareConnection and setting readContexts, but the effect is
> > > the same).
> > >
> > >
> > >
> > > *Boris Pelakh*
> > >
> > > *Ontologist, Developer, Software Architect*
> > >
> > > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> > >
> > > *+1-321-243-3804*
> > >
> > > [image: SemanticArtsLogo]
> > >
> > >
> > >
> >
>

RE: Dataset not applied to queries

Posted by Boris Pelakh <bo...@semanticarts.com>.

Thanks, Puja, that's very helpful. I am making the changes in a forked repo, would I assign pull requests to you once I am finished?

Boris Pelakh
Ontologist, Developer, Software Architect
boris.pelakh@semanticarts.com
+1-321-243-3804


-----Original Message-----
From: Puja Valiyil <pu...@gmail.com> 
Sent: Tuesday, December 4, 2018 10:12 AM
To: dev@rya.incubator.apache.org
Subject: Re: Dataset not applied to queries

Hi Boris,
The execution of the query plan is done by the ParallelEvaluationStrategy:
https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java

It looks like whoever did the rdf4j upgrade updated that class to take the dataset object in its constructor, but it doesn't seem to be used anywhere in query evaluation.  That would be the class to modify,  but I'm still not clear on what the changes would look like since I'm not familiar with what the contract is supposed to be.



On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <bo...@semanticarts.com>
wrote:

> So, a /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph 
> is logically equivalent to
>
> SELECT ...
> FROM <my-named-graph>
> WHERE ...
>
> (overriding whatever FROM/FROM NAMED clauses actually specified in the
> query) I looked at
> org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateIn
> ternal(), and the dataset containing the overriding graph names is 
> passed in, but does not seem to be honored, i.e if I have the 
> following data:
>
> ns:g1 { ns:p1 ns:pred ns:o1 }
> ns:g2 { ns:p2 ns:pred ns:o2 }
>
> and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with 
> default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
>
> I am assuming that there is someplace where the TupleExpr passed to 
> evaluateInternal gets transformed into a scan pattern for Accumulo, 
> after the right index (spo/ops/pso) is identified. If I remember 
> correctly, S/P/O is used the the row ID, and the graph is the column 
> name (or family?). So the dataset should modify the scan filter if applied correctly.
>
> Boris Pelakh
> Ontologist, Developer, Software Architect 
> boris.pelakh@semanticarts.com
> +1-321-243-3804
>
>
> -----Original Message-----
> From: Puja Valiyil <pu...@gmail.com>
> Sent: Tuesday, December 4, 2018 9:31 AM
> To: dev@rya.incubator.apache.org
> Subject: Re: Dataset not applied to queries
>
> Hi Boris,
> Unfortunately I'm not very familiar with that method -- can you 
> provide some more details into exactly what its supposed to do?
> All of the connectors for implementing the sail api are in the 
> rya.sail, and the main classes to look at are RdfCloudTripleStore, 
> RyaSailRepository, and RdfCloudTripleStoreConnection. All of these 
> classes all extend abstract implementations SAIL provides out of the 
> box, so typically the way you extend them to do more stuff is to look 
> at the Sail implementation and customize it for Rya's data structures.
> If you need any help or want to bounce any implementation ideas off of 
> anyone, please send out an email over the dev list. Just let us know 
> how we can help!
> Thanks,
> Puja
>
>
> On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh 
> <boris.pelakh@semanticarts.com
> >
> wrote:
>
> > I am in the process of implementing a SPARQL 1.1-compliant endpoint 
> > for web.rya so that Rya can be used as a federated repository with 
> > RDF4J workbench.
> >
> >
> >
> > One of requirements is to be able to pass default-graph-uri and 
> > named-graph-uri filters external to the query to override the graph 
> > filter in the query itself (see 
> > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> >
> >
> >
> > In the sail API this is accomplished by setting the dataset on the 
> > query object (see 
> > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.
> > ht ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > but that setting does not seem to be honored by the Rya SAIL 
> > implementation. Any ideas on where I can start digging to correct this?
> >
> >
> >
> > (I have also tried wrapping the Rya repository connection in a 
> > ContextAwareConnection and setting readContexts, but the effect is 
> > the same).
> >
> >
> >
> > *Boris Pelakh*
> >
> > *Ontologist, Developer, Software Architect*
> >
> > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> >
> > *+1-321-243-3804*
> >
> > [image: SemanticArtsLogo]
> >
> >
> >
>

Re: Dataset not applied to queries

Posted by Puja Valiyil <pu...@gmail.com>.

Hi Boris,
The execution of the query plan is done by the ParallelEvaluationStrategy:
https://github.com/apache/incubator-rya/blob/master/sail/src/main/java/org/apache/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java

It looks like whoever did the rdf4j upgrade updated that class to take the
dataset object in its constructor, but it doesn't seem to be used anywhere
in query evaluation.  That would be the class to modify,  but I'm still not
clear on what the changes would look like since I'm not familiar with what
the contract is supposed to be.



On Tue, Dec 4, 2018 at 9:45 AM Boris Pelakh <bo...@semanticarts.com>
wrote:

> So, a /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph is
> logically equivalent to
>
> SELECT ...
> FROM <my-named-graph>
> WHERE ...
>
> (overriding whatever FROM/FROM NAMED clauses actually specified in the
> query) I looked at
> org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateInternal(),
> and the dataset containing the overriding graph names is passed in, but
> does not seem to be honored, i.e if I have the following data:
>
> ns:g1 { ns:p1 ns:pred ns:o1 }
> ns:g2 { ns:p2 ns:pred ns:o2 }
>
> and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with
> default-graph-uri set to ns:g1, I expect to get 1, but I get 2.
>
> I am assuming that there is someplace where the TupleExpr passed to
> evaluateInternal gets transformed into a scan pattern for Accumulo, after
> the right index (spo/ops/pso) is identified. If I remember correctly, S/P/O
> is used the the row ID, and the graph is the column name (or family?). So
> the dataset should modify the scan filter if applied correctly.
>
> Boris Pelakh
> Ontologist, Developer, Software Architect
> boris.pelakh@semanticarts.com
> +1-321-243-3804
>
>
> -----Original Message-----
> From: Puja Valiyil <pu...@gmail.com>
> Sent: Tuesday, December 4, 2018 9:31 AM
> To: dev@rya.incubator.apache.org
> Subject: Re: Dataset not applied to queries
>
> Hi Boris,
> Unfortunately I'm not very familiar with that method -- can you provide
> some more details into exactly what its supposed to do?
> All of the connectors for implementing the sail api are in the rya.sail,
> and the main classes to look at are RdfCloudTripleStore, RyaSailRepository,
> and RdfCloudTripleStoreConnection. All of these classes all extend abstract
> implementations SAIL provides out of the box, so typically the way you
> extend them to do more stuff is to look at the Sail implementation and
> customize it for Rya's data structures.
> If you need any help or want to bounce any implementation ideas off of
> anyone, please send out an email over the dev list. Just let us know how we
> can help!
> Thanks,
> Puja
>
>
> On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh <boris.pelakh@semanticarts.com
> >
> wrote:
>
> > I am in the process of implementing a SPARQL 1.1-compliant endpoint
> > for web.rya so that Rya can be used as a federated repository with
> > RDF4J workbench.
> >
> >
> >
> > One of requirements is to be able to pass default-graph-uri and
> > named-graph-uri filters external to the query to override the graph
> > filter in the query itself (see
> > https://www.w3.org/TR/sparql11-protocol/#query-operation).
> >
> >
> >
> > In the sail API this is accomplished by setting the dataset on the
> > query object (see
> > http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.ht
> > ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> > but that setting does not seem to be honored by the Rya SAIL
> > implementation. Any ideas on where I can start digging to correct this?
> >
> >
> >
> > (I have also tried wrapping the Rya repository connection in a
> > ContextAwareConnection and setting readContexts, but the effect is the
> > same).
> >
> >
> >
> > *Boris Pelakh*
> >
> > *Ontologist, Developer, Software Architect*
> >
> > *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
> >
> > *+1-321-243-3804*
> >
> > [image: SemanticArtsLogo]
> >
> >
> >
>

RE: Dataset not applied to queries

Posted by Boris Pelakh <bo...@semanticarts.com>.

So, a /sparql?query=SELECT...WHERE...&default-graph-uri=my-named-graph is logically equivalent to 

SELECT ...
FROM <my-named-graph>
WHERE ...

(overriding whatever FROM/FROM NAMED clauses actually specified in the query) I looked at org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection.evaluateInternal(), and the dataset containing the overriding graph names is passed in, but does not seem to be honored, i.e if I have the following data:

ns:g1 { ns:p1 ns:pred ns:o1 }
ns:g2 { ns:p2 ns:pred ns:o2 }

and I execute 'SELECT COUNT(?s) where { ?s ns:pred ?o }' with default-graph-uri set to ns:g1, I expect to get 1, but I get 2.

I am assuming that there is someplace where the TupleExpr passed to evaluateInternal gets transformed into a scan pattern for Accumulo, after the right index (spo/ops/pso) is identified. If I remember correctly, S/P/O is used the the row ID, and the graph is the column name (or family?). So the dataset should modify the scan filter if applied correctly.

Boris Pelakh
Ontologist, Developer, Software Architect
boris.pelakh@semanticarts.com
+1-321-243-3804

-----Original Message-----
From: Puja Valiyil <pu...@gmail.com> 
Sent: Tuesday, December 4, 2018 9:31 AM
To: dev@rya.incubator.apache.org
Subject: Re: Dataset not applied to queries

Hi Boris,
Unfortunately I'm not very familiar with that method -- can you provide some more details into exactly what its supposed to do?
All of the connectors for implementing the sail api are in the rya.sail, and the main classes to look at are RdfCloudTripleStore, RyaSailRepository, and RdfCloudTripleStoreConnection. All of these classes all extend abstract implementations SAIL provides out of the box, so typically the way you extend them to do more stuff is to look at the Sail implementation and customize it for Rya's data structures.
If you need any help or want to bounce any implementation ideas off of anyone, please send out an email over the dev list. Just let us know how we can help!
Thanks,
Puja

On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh <bo...@semanticarts.com>
wrote:

> I am in the process of implementing a SPARQL 1.1-compliant endpoint 
> for web.rya so that Rya can be used as a federated repository with 
> RDF4J workbench.
>
>
>
> One of requirements is to be able to pass default-graph-uri and 
> named-graph-uri filters external to the query to override the graph 
> filter in the query itself (see 
> https://www.w3.org/TR/sparql11-protocol/#query-operation).
>
>
>
> In the sail API this is accomplished by setting the dataset on the 
> query object (see 
> http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.ht
> ml#setDataset-org.eclipse.rdf4j.query.Dataset-),
> but that setting does not seem to be honored by the Rya SAIL 
> implementation. Any ideas on where I can start digging to correct this?
>
>
>
> (I have also tried wrapping the Rya repository connection in a 
> ContextAwareConnection and setting readContexts, but the effect is the 
> same).
>
>
>
> *Boris Pelakh*
>
> *Ontologist, Developer, Software Architect*
>
> *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
>
> *+1-321-243-3804*
>
> [image: SemanticArtsLogo]
>
>
>

Re: Dataset not applied to queries

Posted by Puja Valiyil <pu...@gmail.com>.

Hi Boris,
Unfortunately I'm not very familiar with that method -- can you provide
some more details into exactly what its supposed to do?
All of the connectors for implementing the sail api are in the rya.sail,
and the main classes to look at are RdfCloudTripleStore, RyaSailRepository,
and RdfCloudTripleStoreConnection. All of these classes all extend abstract
implementations SAIL provides out of the box, so typically the way you
extend them to do more stuff is to look at the Sail implementation and
customize it for Rya's data structures.
If you need any help or want to bounce any implementation ideas off of
anyone, please send out an email over the dev list. Just let us know how we
can help!
Thanks,
Puja

On Tue, Dec 4, 2018 at 9:19 AM Boris Pelakh <bo...@semanticarts.com>
wrote:

> I am in the process of implementing a SPARQL 1.1-compliant endpoint for
> web.rya so that Rya can be used as a federated repository with RDF4J
> workbench.
>
>
>
> One of requirements is to be able to pass default-graph-uri and
> named-graph-uri filters external to the query to override the graph filter
> in the query itself (see
> https://www.w3.org/TR/sparql11-protocol/#query-operation).
>
>
>
> In the sail API this is accomplished by setting the dataset on the query
> object (see
> http://docs.rdf4j.org/javadoc/2.2/org/eclipse/rdf4j/query/Operation.html#setDataset-org.eclipse.rdf4j.query.Dataset-),
> but that setting does not seem to be honored by the Rya SAIL
> implementation. Any ideas on where I can start digging to correct this?
>
>
>
> (I have also tried wrapping the Rya repository connection in a
> ContextAwareConnection and setting readContexts, but the effect is the
> same).
>
>
>
> *Boris Pelakh*
>
> *Ontologist, Developer, Software Architect*
>
> *boris.pelakh@semanticarts.com <bo...@semanticarts.com>*
>
> *+1-321-243-3804*
>
> [image: SemanticArtsLogo]
>
>
>