On 02/12/2019 16:44, Nouwt, B. (Barry) wrote:
Hey Andy,

It's easy. I just convert the graph pattern (ElementPathBlock) into a 
DefaultDirectedGraph 
(https://jgrapht.org/javadoc/org/jgrapht/graph/DefaultDirectedGraph.html) and 
add the correct edge/vertex comparators. With the two graphs and the two 
comparators, you instantiate the class VF2GraphIsomorphismInspector 
(https://jgrapht.org/javadoc/org/jgrapht/alg/isomorphism/VF2GraphIsomorphismInspector.html)
 and you can iterate over the isomorphisms/mappings.

The only catch was that I could not use Jena's Node instances directly as edge 
objects in JGraphT (I could do this with the vertices), because their equals 
was too 'smart' for this purpose.

Straight into RDF* territory!

The URI of a property in a triple isn't identifying the triple; it is the "class" of the edge, not the edge itself. The edge is the three parts S-P-O.

Jena now has Node_Triple (experimental) to support work on extensions to RDF (and Node_Graph)

This is what RDF* adds. It is either (RDF* PG mode - like property graphs) adding triples into the RDF data model as a new kind of RDF Term (in fact its abstractly a literal - it describes itself), or it is (RDF* SA mode) a reference to a triple which may, or may not, be in the graph; that's closer to reification.

    Andy

If you want I can add the JGraphT code in the github repo as well.

Regards, Barry

-----Original Message-----
From: Andy Seaborne <a...@apache.org>
Sent: maandag 2 december 2019 14:32
To: users@jena.apache.org
Subject: Re: ElementPathBlock comparison

Hi Barry,

How easy is it to use JGraphT with Jena?

I'd be very interested in hearing about your experiences.

      Andy

On 02/12/2019 10:43, Nouwt, B. (Barry) wrote:
Hey Andy, thanks for the quick responses.

For the time being I'm using JGraphT's isomorphism algorithm (VF2) and it works 
as expected.

See: https://jgrapht.org/guide/UserOverview#graph-comparisons

I might retry IsoMatcher/IsoAlg in the future.

Regards, Barry

-----Original Message-----
From: Andy Seaborne <a...@apache.org>
Sent: zondag 1 december 2019 10:58
To: users@jena.apache.org
Subject: Re: ElementPathBlock comparison

Barry,

Pull request #642 should fix this.

Either do the variable -> blank node replacement and call
IsoMatcher.isomorphic(graph,graph)


Or call the isomorphism algorithm code as follows:

     Iso.Mappable mappable = (n1,n2) ->
       ( n1.isBlank() && n2.isBlank())
       || ( n1.isVariable() && n2.isVariable() );

     List<Tuple<Node>> x1 = ...
     List<Tuple<Node>> x2 = ...

     boolean b =
       IsoAlg.isIsomorphic(x1, x2, mappable, NodeUtils.sameValue);

The "mappable" is the rule for which terms are considered in the isomorphism. 
The default and used by the main public functions is bnode mapping.

IsoMatcher itself as a class is deprecated (its still there) and everything is 
done with functions.

       Andy

[1] https://github.com/apache/jena/pull/642

On 29/11/2019 12:16, Andy Seaborne wrote:
Barry,

It does look like something is wrong in iso-matching. Recorded as
JENA-1789.

Using graph1.isoIsomorphicWith(graph2)

is a workaround.

IsoMatcher "fails safe" for its use in the test suite and also its
used there mainly on ResultSets not graphs.

      Andy


On 28/11/2019 16:04, Nouwt, B. (Barry) wrote:
Hi Andy, thanks for the effort.

If you clone this public github repository
(https://github.com/barrynl/jena-example) and set it us as a Maven
project and execute the main() in this Java class:

https://github.com/barrynl/jena-example/blob/master/src/main/java/nl
/ tno/ict/ds/cb/jena/JenaIsomorphTest.java


it will show how converting variable nodes to blank nodes and using
the IsoMatcher yields true, while it should be false.

Maybe you can find what I'm doing wrong.

Thanks in advance!

Barry

-----Original Message-----
From: Andy Seaborne <a...@apache.org>
Sent: donderdag 28 november 2019 11:22
To: users@jena.apache.org
Subject: Re: ElementPathBlock comparison



On 25/11/2019 13:52, Nouwt, B. (Barry) wrote:
Hey Andy,

I have another question about comparing ElementPathBlock's the way
you suggest below using IsoMatcher.

The following two graph patterns should (in my opinion and for my
use
case) not be the same, but the IsoMatcher says they match:

graphpattern1: ?a <http://www.tno.nl/test1> ?b . ?b
<http://www.tno.nl/test2> ?a .

graphpattern2: ?a <http://www.tno.nl/test1> ?b . ?a
<http://www.tno.nl/test2> ?b .

They should be different.

If it's _:a and _:b is it different? In which case the variable bit
is wrong.


Since RDF triples form a directed graph, this result surprises me,
because in graphpattern1 the subject of /test1 has a single
outgoing edge, while in graphpattern2 the subject of /test1 has two
outgoing edges. How can this be judged the same?

I've tested it in two ways:
- converting all variables to blank nodes and using:
IsoMatcher match = new IsoMatcher(tuplesTriples(gr1.find()),
tuplesTriples(gr2.find()), new
ResultSetCompare.BNodeIso(NodeUtils.sameValue));

- or not converting them to blank nodes and using:
IsoMatcher match = new IsoMatcher(tuplesTriples(gr1.find()),
tuplesTriples(gr2.find()), new
CustomBNodeIso(NodeUtils.sameValue));

Where CustomBNodeIso adds the IF statement you suggest below.

In both cases the above two graph patterns are judged the same
while they shouldn't.

Any idea what I'm doing wrong?

Do you have a complete, mininal example I can copy-and-paste and run?

If uou put it on a gist/pastebin I might find time to try it.

        Andy


Regards, Barry

-----Original Message-----
From: Nouwt, B. (Barry) <barry.no...@tno.nl.INVALID>
Sent: donderdag 21 november 2019 13:03
To: users@jena.apache.org
Subject: RE: ElementPathBlock comparison

Hey Andy, thanks. I'm currently testing the IsoMatcher -
EqualityTest combination and the first tests look promising.

I use the following code (where the gr1 and gr2 graphs have all
variables of the graph pattern replaced by blanknodes):

IsoMatcher match = new IsoMatcher(tuplesTriples(gr1.find()),
tuplesTriples(gr2.find()), new
ResultSetCompare.BNodeIso(NodeUtils.sameValue));

but as I said, it requires some more testing. Not having to convert
the variable into blanknodes would probably be more elegant, so
maybe I'll try your suggestion below as well.

Regards,

Barry

-----Original Message-----
From: Andy Seaborne <a...@apache.org>
Sent: woensdag 20 november 2019 10:41
To: users@jena.apache.org
Subject: Re: ElementPathBlock comparison



On 19/11/2019 15:52, Nouwt, B. (Barry) wrote:
Hi Andy, I have an additional question regarding your tip about
turning variables into blanknodes with names; would that also work
in case of predicates? Because variables can be located at the
'predicate' location of a triple, but I'm unsure whether
blanknodes are allowed at that location.

Yes.

My recommendation is to write a EqualityTest that does variable
isomorphism.  It's a small chnage to the

Copy BNodeIso and add the "if":

                 if ( n1.isVariable() && n2.isVariable() )
                     return mapping.makeIsomorphic(n1, n2) ;

(not tested)

         Andy


Regards, Barry

-----Original Message-----
From: Nouwt, B. (Barry) <barry.no...@tno.nl.INVALID>
Sent: dinsdag 19 november 2019 16:49
To: users@jena.apache.org
Subject: RE: ElementPathBlock comparison

Thanks for the quick replies.

@Andy Exactly, I do care about the shape, but not about exact
variable names.

I wanted to use Google Guava Graph library to construct the graphs
and use their equality mechanism, but I think the IsoMatcher is a
better fit, thanks for the pointer! This together with your tip
about transforming the same variable nodes into blank nodes with
the same name, it might just work in combination with BNodeIso.
I'll give that a try and report back the result.

BTW In the comments of this IsoMatcher class, it says "For graphs,
the Graph isomorphism code in Jena is much better (better tested,
better performance)", is this relevant for me? And do you know
which isomorphism code in Jena is it referring to?

@Martynas I could, indeed, encode the two BGPs into two RDF graphs
using sp:TriplePattern, but then I still a way to match them. For
my problem this RDF encoding is not necessary and encoding it
using the Google Guava Graph lib seems sufficient.

Regards, Barry

-----Original Message-----
From: Andy Seaborne <a...@apache.org>
Sent: dinsdag 19 november 2019 15:49
To: users@jena.apache.org
Subject: Re: ElementPathBlock comparison


Hi all,

I have two ARQ ElementPathBlocks (or Basic Graph Pattern, see
SPARQL spec https://www.w3.org/TR/sparql11-query/#GraphPattern)
and would like to know whether they are equal ignoring variable
names and ordering of the triples. What is the best/easiest way
to do that with the Apache Jena? I see there is an
org.apache.jena.sparql.util.Iso class that provides methods for
testing isomorphisms...but I'm unsure whether this is what I am
looking for. I also tested two ElementPathBlocks and using their
equalTo method (which uses the Iso class), but both variable
names and order seems to matter judging them equal.

I'm guessing you mean not caring about the variable names but
respecting the shape they create in the BGP.

IsoMatcher is a simple algorithm for matching unordered lists
(Iso.isomorphic is ordered lists.)

If you want to ignore variables names you'll need a "EqualityTest"
that captures that


BNodeIso does this for bnodes.  Modifying that for a Var->Var map
loosk possible (or converting the input BGPs to have a bnode with
label derived from the Variable name).

          Andy
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