Hi Delaram, I have loaded your sample dataset into a latest Virtuoso 7.2.2 open source database (once missing prefixes haad been added) and both queries run successfully, although query_3 returns no results. Is the a reason you are running 7.2.1 and can you update to the latest 7.2.2 version available in git ?
SQL> DB.DBA.TTLP_MT (file_to_string_output('./delaram.ttl'), '','delaram',0);
Done. -- 44 msec.
SQL> sparql select count(*) from <delaram> where {?s ?p ?o};
callret-0
INTEGER
_______________________________________________________________________________
765
1 Rows. -- 12 msec.
SQL>
SQL> SPARQL PREFIX : <http://gmmo.uga.edu/#>
Type the rest of statement, end with a semicolon (;)> PREFIX rdf:
<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
Type the rest of statement, end with a semicolon (;)> PREFIX owl:
<http://www.w3.org/2002/07/owl#>
Type the rest of statement, end with a semicolon (;)> PREFIX rdfs:
<http://www.w3.org/2000/01/rdf-schema#>
Type the rest of statement, end with a semicolon (;)> PREFIX xsd:
<http://www.w3.org/2001/XMLSchema#>
Type the rest of statement, end with a semicolon (;)> SELECT ?pdb WHERE {
Type the rest of statement, end with a semicolon (;)> ?oligo0:hasRoot?mono0.
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_ring_atom2.
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
:ringIndex "2".
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
:hasSideAtom ?mono0_side_atom2 .
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom2:sideIndex "2".
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom2:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_ring_atom3.
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
:ringIndex "3".
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
:hasSideAtom ?mono0_side_atom3 .
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom3:sideIndex "3".
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom3:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_ring_atom4.
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
:ringIndex "4".
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
:hasSideAtom ?mono0_side_atom4 .
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom4:sideIndex "4".
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom4:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_last_c.
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
:ringIndex "5".
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
:hasSideAtom ?mono0_last_c_side_atom.
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c_side_atom
:sideIndex "+1".
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c_side_atom
:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?oligo1:hasRoot?mono1.
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_anomeric.
Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
:ringIndex "1".
Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
:hasSideAtom ?mono1_anomeric_side_atom .
Type the rest of statement, end with a semicolon (;)>
?mono1_anomeric_side_atom:sideIndex "1".
Type the rest of statement, end with a semicolon (;)>
?mono1_anomeric_side_atom:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_ring_atom2.
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
:ringIndex "2".
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
:hasSideAtom ?mono1_side_atom2 .
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom2:sideIndex "2".
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom2:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_ring_atom3.
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
:ringIndex "3".
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
:hasSideAtom ?mono1_side_atom3 .
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom3:sideIndex "3".
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom3:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_ring_atom4.
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
:ringIndex "4".
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
:hasSideAtom ?mono1_side_atom4 .
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom4:sideIndex "4".
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom4:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_last_c.
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
:ringIndex "5".
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
:hasSideAtom ?mono1_last_c_side_atom.
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c_side_atom
:sideIndex "+1".
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c_side_atom
:orientation"Up".
Type the rest of statement, end with a semicolon (;)> {
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
?oligo0.
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
?oligo1.
Type the rest of statement, end with a semicolon (;)> } UNION {
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
?oligo1.
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
?oligo0.
Type the rest of statement, end with a semicolon (;)> }
Type the rest of statement, end with a semicolon (;)> ?pdb :hasOligo
?oligo0.
Type the rest of statement, end with a semicolon (;)> ?pdb :hasOligo
?oligo1.
Type the rest of statement, end with a semicolon (;)> }
Type the rest of statement, end with a semicolon (;)> ;
pdb
LONG VARCHAR
_______________________________________________________________________________
http://gmmo.uga.edu/#sample
http://gmmo.uga.edu/#sample
2 Rows. -- 6516 msec.
SQL>
SQL> SPARQL PREFIX : <http://gmmo.uga.edu/#>
Type the rest of statement, end with a semicolon (;)> PREFIX rdf:
<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
Type the rest of statement, end with a semicolon (;)> PREFIX owl:
<http://www.w3.org/2002/07/owl#>
Type the rest of statement, end with a semicolon (;)> PREFIX rdfs:
<http://www.w3.org/2000/01/rdf-schema#>
Type the rest of statement, end with a semicolon (;)> PREFIX xsd:
<http://www.w3.org/2001/XMLSchema#>
Type the rest of statement, end with a semicolon (;)> SELECT ?pdb WHERE {
Type the rest of statement, end with a semicolon (;)> ?oligo0:hasRoot?mono0.
Type the rest of statement, end with a semicolon (;)> ?mono0 :hasRingAtom
?mono0_ring_atom2.
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
:ringIndex "2".
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
:hasSideAtom ?mono0_side_atom2 .
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom2:sideIndex "2".
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom2:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_ring_atom3.
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
:ringIndex "3".
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
:hasSideAtom ?mono0_side_atom3 .
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom3:sideIndex "3".
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom3:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_ring_atom4.
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
:ringIndex "4".
Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
:hasSideAtom ?mono0_side_atom4 .
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom4:sideIndex "4".
Type the rest of statement, end with a semicolon (;)>
?mono0_side_atom4:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono0
:hasRingAtom?mono0_last_c.
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
:ringIndex "5".
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
:hasSideAtom ?mono0_last_c_side_atom.
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c_side_atom
:sideIndex "+1".
Type the rest of statement, end with a semicolon (;)> ?mono0_last_c_side_atom
:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?oligo1:hasRoot?mono1.
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_anomeric.
Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
:ringIndex "1".
Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
:hasSideAtom ?mono1_anomeric_side_atom .
Type the rest of statement, end with a semicolon (;)>
?mono1_anomeric_side_atom:sideIndex "1".
Type the rest of statement, end with a semicolon (;)>
?mono1_anomeric_side_atom:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_ring_atom2.
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
:ringIndex "2".
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
:hasSideAtom ?mono1_side_atom2 .
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom2:sideIndex "2".
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom2:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_ring_atom3.
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
:ringIndex "3".
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
:hasSideAtom ?mono1_side_atom3 .
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom3:sideIndex "3".
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom3:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_ring_atom4.
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
:ringIndex "4".
Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
:hasSideAtom ?mono1_side_atom4 .
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom4:sideIndex "4".
Type the rest of statement, end with a semicolon (;)>
?mono1_side_atom4:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono1
:hasRingAtom?mono1_last_c.
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
:ringIndex "5".
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
:hasSideAtom ?mono1_last_c_side_atom.
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c_side_atom
:sideIndex "+1".
Type the rest of statement, end with a semicolon (;)> ?mono1_last_c_side_atom
:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?oligo2:hasRoot?mono2.
Type the rest of statement, end with a semicolon (;)> ?mono2
:hasRingAtom?mono2_anomeric.
Type the rest of statement, end with a semicolon (;)> ?mono2_anomeric
:ringIndex "1".
Type the rest of statement, end with a semicolon (;)> ?mono2_anomeric
:hasSideAtom ?mono2_anomeric_side_atom .
Type the rest of statement, end with a semicolon (;)>
?mono2_anomeric_side_atom:sideIndex "1".
Type the rest of statement, end with a semicolon (;)>
?mono2_anomeric_side_atom:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono2
:hasRingAtom?mono2_ring_atom2.
Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom2
:ringIndex "2".
Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom2
:hasSideAtom ?mono2_side_atom2 .
Type the rest of statement, end with a semicolon (;)>
?mono2_side_atom2:sideIndex "2".
Type the rest of statement, end with a semicolon (;)>
?mono2_side_atom2:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono2
:hasRingAtom?mono2_ring_atom3.
Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom3
:ringIndex "3".
Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom3
:hasSideAtom ?mono2_side_atom3 .
Type the rest of statement, end with a semicolon (;)>
?mono2_side_atom3:sideIndex "3".
Type the rest of statement, end with a semicolon (;)>
?mono2_side_atom3:orientation"Up".
Type the rest of statement, end with a semicolon (;)> ?mono2
:hasRingAtom?mono2_ring_atom4.
Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom4
:ringIndex "4".
Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom4
:hasSideAtom ?mono2_side_atom4 .
Type the rest of statement, end with a semicolon (;)>
?mono2_side_atom4:sideIndex "4".
Type the rest of statement, end with a semicolon (;)>
?mono2_side_atom4:orientation"Down".
Type the rest of statement, end with a semicolon (;)> ?mono2
:hasRingAtom?mono2_last_c.
Type the rest of statement, end with a semicolon (;)> ?mono2_last_c
:ringIndex "5".
Type the rest of statement, end with a semicolon (;)> ?mono2_last_c
:hasSideAtom ?mono2_last_c_side_atom.
Type the rest of statement, end with a semicolon (;)> ?mono2_last_c_side_atom
:sideIndex "+1".
Type the rest of statement, end with a semicolon (;)> ?mono2_last_c_side_atom
:orientation"Up".
Type the rest of statement, end with a semicolon (;)> {
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
?oligo0.
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
?oligo1.
Type the rest of statement, end with a semicolon (;)> } UNION {
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
?oligo1.
Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
?oligo0.
Type the rest of statement, end with a semicolon (;)> }
Type the rest of statement, end with a semicolon (;)> {
Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasParent
?oligo1.
Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasChild
?oligo2.
Type the rest of statement, end with a semicolon (;)> } UNION {
Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasParent
?oligo2.
Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasChild
?oligo1.
Type the rest of statement, end with a semicolon (;)> }
Type the rest of statement, end with a semicolon (;)> ?pdb :hasOligo
?oligo0.
Type the rest of statement, end with a semicolon (;)> ?pdb :hasOligo
?oligo1.
Type the rest of statement, end with a semicolon (;)> ?pdb :hasOligo
?oligo2.
Type the rest of statement, end with a semicolon (;)> }
Type the rest of statement, end with a semicolon (;)> ;
pdb
LONG VARCHAR
_______________________________________________________________________________
0 Rows. -- 35524 msec.
SQL>
SQL> status('');
REPORT
VARCHAR
_______________________________________________________________________________
OpenLink Virtuoso Server
Version 07.20.3216-pthreads for Darwin as of Mar 2 2016
Started on: 2016-03-04 02:14 GMT+0
Best Regards
Hugh Williams
Professional Services
OpenLink Software, Inc. // http://www.openlinksw.com/
Weblog -- http://www.openlinksw.com/blogs/
LinkedIn -- http://www.linkedin.com/company/openlink-software/
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Facebook -- http://www.facebook.com/OpenLinkSoftware
Universal Data Access, Integration, and Management Technology Providers
> On 4 Mar 2016, at 15:44, Delaram Ra <delaram...@gmail.com> wrote:
>
> Hi all,
>
> I ran into this problem recently, my program generates queries that sometimes
> are too long. When I try to execute these queries on virtuoso (7.2.1) it
> gives me the following error:
> Virtuoso 42000 Error SR483: Stack Overflow
> I have attached the sample RDF graph that I'm trying to query and the sample
> queries as well. One of them tries to find 2 attached structures (works fine)
> and the other tries to find 3 attached structures (this is when error
> happens).
> I have checked the semantics of the queries and they seem fine to me.
> So I'm wondering if the error is related to length of the query? or it is
> something else?
>
> Any suggestion/help is appreciated.
>
> Best,
> Delaram
> <query_2structures.txt><test.ttl><query_3structures.txt>------------------------------------------------------------------------------
> _______________________________________________
> Virtuoso-users mailing list
> Virtuoso-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
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