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
PREFIX : <http://gmmo.uga.edu/#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?pdb WHERE { ?oligo0 :hasRoot ?mono0. ?mono0 :hasRingAtom ?mono0_ring_atom2. ?mono0_ring_atom2 :ringIndex "2". ?mono0_ring_atom2 :hasSideAtom ?mono0_side_atom2 . ?mono0_side_atom2 :sideIndex "2". ?mono0_side_atom2 :orientation "Down". ?mono0 :hasRingAtom ?mono0_ring_atom3. ?mono0_ring_atom3 :ringIndex "3". ?mono0_ring_atom3 :hasSideAtom ?mono0_side_atom3 . ?mono0_side_atom3 :sideIndex "3". ?mono0_side_atom3 :orientation "Up". ?mono0 :hasRingAtom ?mono0_ring_atom4. ?mono0_ring_atom4 :ringIndex "4". ?mono0_ring_atom4 :hasSideAtom ?mono0_side_atom4 . ?mono0_side_atom4 :sideIndex "4". ?mono0_side_atom4 :orientation "Down". ?mono0 :hasRingAtom ?mono0_last_c. ?mono0_last_c :ringIndex "5". ?mono0_last_c :hasSideAtom ?mono0_last_c_side_atom. ?mono0_last_c_side_atom :sideIndex "+1". ?mono0_last_c_side_atom :orientation "Up". ?oligo1 :hasRoot ?mono1. ?mono1 :hasRingAtom ?mono1_anomeric. ?mono1_anomeric :ringIndex "1". ?mono1_anomeric :hasSideAtom ?mono1_anomeric_side_atom . ?mono1_anomeric_side_atom :sideIndex "1". ?mono1_anomeric_side_atom :orientation "Up". ?mono1 :hasRingAtom ?mono1_ring_atom2. ?mono1_ring_atom2 :ringIndex "2". ?mono1_ring_atom2 :hasSideAtom ?mono1_side_atom2 . ?mono1_side_atom2 :sideIndex "2". ?mono1_side_atom2 :orientation "Down". ?mono1 :hasRingAtom ?mono1_ring_atom3. ?mono1_ring_atom3 :ringIndex "3". ?mono1_ring_atom3 :hasSideAtom ?mono1_side_atom3 . ?mono1_side_atom3 :sideIndex "3". ?mono1_side_atom3 :orientation "Up". ?mono1 :hasRingAtom ?mono1_ring_atom4. ?mono1_ring_atom4 :ringIndex "4". ?mono1_ring_atom4 :hasSideAtom ?mono1_side_atom4 . ?mono1_side_atom4 :sideIndex "4". ?mono1_side_atom4 :orientation "Down". ?mono1 :hasRingAtom ?mono1_last_c. ?mono1_last_c :ringIndex "5". ?mono1_last_c :hasSideAtom ?mono1_last_c_side_atom. ?mono1_last_c_side_atom :sideIndex "+1". ?mono1_last_c_side_atom :orientation "Up". { ?linkage0 :hasParent ?oligo0. ?linkage0 :hasChild ?oligo1. } UNION { ?linkage0 :hasParent ?oligo1. ?linkage0 :hasChild ?oligo0. } ?pdb :hasOligo ?oligo0. ?pdb :hasOligo ?oligo1. }
test.ttl
Description: Binary data
PREFIX : <http://gmmo.uga.edu/#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?pdb WHERE { ?oligo0 :hasRoot ?mono0. ?mono0 :hasRingAtom ?mono0_ring_atom2. ?mono0_ring_atom2 :ringIndex "2". ?mono0_ring_atom2 :hasSideAtom ?mono0_side_atom2 . ?mono0_side_atom2 :sideIndex "2". ?mono0_side_atom2 :orientation "Down". ?mono0 :hasRingAtom ?mono0_ring_atom3. ?mono0_ring_atom3 :ringIndex "3". ?mono0_ring_atom3 :hasSideAtom ?mono0_side_atom3 . ?mono0_side_atom3 :sideIndex "3". ?mono0_side_atom3 :orientation "Up". ?mono0 :hasRingAtom ?mono0_ring_atom4. ?mono0_ring_atom4 :ringIndex "4". ?mono0_ring_atom4 :hasSideAtom ?mono0_side_atom4 . ?mono0_side_atom4 :sideIndex "4". ?mono0_side_atom4 :orientation "Down". ?mono0 :hasRingAtom ?mono0_last_c. ?mono0_last_c :ringIndex "5". ?mono0_last_c :hasSideAtom ?mono0_last_c_side_atom. ?mono0_last_c_side_atom :sideIndex "+1". ?mono0_last_c_side_atom :orientation "Up". ?oligo1 :hasRoot ?mono1. ?mono1 :hasRingAtom ?mono1_anomeric. ?mono1_anomeric :ringIndex "1". ?mono1_anomeric :hasSideAtom ?mono1_anomeric_side_atom . ?mono1_anomeric_side_atom :sideIndex "1". ?mono1_anomeric_side_atom :orientation "Up". ?mono1 :hasRingAtom ?mono1_ring_atom2. ?mono1_ring_atom2 :ringIndex "2". ?mono1_ring_atom2 :hasSideAtom ?mono1_side_atom2 . ?mono1_side_atom2 :sideIndex "2". ?mono1_side_atom2 :orientation "Down". ?mono1 :hasRingAtom ?mono1_ring_atom3. ?mono1_ring_atom3 :ringIndex "3". ?mono1_ring_atom3 :hasSideAtom ?mono1_side_atom3 . ?mono1_side_atom3 :sideIndex "3". ?mono1_side_atom3 :orientation "Up". ?mono1 :hasRingAtom ?mono1_ring_atom4. ?mono1_ring_atom4 :ringIndex "4". ?mono1_ring_atom4 :hasSideAtom ?mono1_side_atom4 . ?mono1_side_atom4 :sideIndex "4". ?mono1_side_atom4 :orientation "Down". ?mono1 :hasRingAtom ?mono1_last_c. ?mono1_last_c :ringIndex "5". ?mono1_last_c :hasSideAtom ?mono1_last_c_side_atom. ?mono1_last_c_side_atom :sideIndex "+1". ?mono1_last_c_side_atom :orientation "Up". ?oligo2 :hasRoot ?mono2. ?mono2 :hasRingAtom ?mono2_anomeric. ?mono2_anomeric :ringIndex "1". ?mono2_anomeric :hasSideAtom ?mono2_anomeric_side_atom . ?mono2_anomeric_side_atom :sideIndex "1". ?mono2_anomeric_side_atom :orientation "Up". ?mono2 :hasRingAtom ?mono2_ring_atom2. ?mono2_ring_atom2 :ringIndex "2". ?mono2_ring_atom2 :hasSideAtom ?mono2_side_atom2 . ?mono2_side_atom2 :sideIndex "2". ?mono2_side_atom2 :orientation "Up". ?mono2 :hasRingAtom ?mono2_ring_atom3. ?mono2_ring_atom3 :ringIndex "3". ?mono2_ring_atom3 :hasSideAtom ?mono2_side_atom3 . ?mono2_side_atom3 :sideIndex "3". ?mono2_side_atom3 :orientation "Up". ?mono2 :hasRingAtom ?mono2_ring_atom4. ?mono2_ring_atom4 :ringIndex "4". ?mono2_ring_atom4 :hasSideAtom ?mono2_side_atom4 . ?mono2_side_atom4 :sideIndex "4". ?mono2_side_atom4 :orientation "Down". ?mono2 :hasRingAtom ?mono2_last_c. ?mono2_last_c :ringIndex "5". ?mono2_last_c :hasSideAtom ?mono2_last_c_side_atom. ?mono2_last_c_side_atom :sideIndex "+1". ?mono2_last_c_side_atom :orientation "Up". { ?linkage0 :hasParent ?oligo0. ?linkage0 :hasChild ?oligo1. } UNION { ?linkage0 :hasParent ?oligo1. ?linkage0 :hasChild ?oligo0. } { ?linkage1 :hasParent ?oligo1. ?linkage1 :hasChild ?oligo2. } UNION { ?linkage1 :hasParent ?oligo2. ?linkage1 :hasChild ?oligo1. } ?pdb :hasOligo ?oligo0. ?pdb :hasOligo ?oligo1. ?pdb :hasOligo ?oligo2. }
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