Dear Virtuosans,
I noticed that queries can be much slower when using variables as
properties (even if the variable can only have one value) e.g.:
DATA (extract):
:display :startRelation :posStart.
:gene0 rdf:type :Gene.
:gene0 :posStart "53416"^^xsd:numeric.
:gene1 rdf:type :Gene.
:gene1 :posStart "29513"^^xsd:numeric.
...
SIMPLE QUERY:
?gene :posStart ?start.
SLOWER QUERY:
:display :startRelation ?startRel.
?gene ?startRel ?start.
I assume that the query engine first tries to match the "?gene
?startRel ?start" constraint, whereas begining by ":display
:startRelation ?startRel." would define the value of ?startRel which
would be used to find the start positions of the genes.
I can live with the simple query, but the second one would make the
development of our application easier. Is there anything we could do to
improve the performance of the second query?
Thank you!
kind regards
Olivier Dameron
NB: for the record, below is the script I used for generating the
dataset, as well as the two queries
===== generateDataSet.py
#! /usr/bin/env python
import random
nbGenes = 50000
geneLengthMax = 100
chromosomeLength = 100000
with open("debugDataset.ttl", "w") as dataFile:
dataFile.write("""
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix : <http://www.univ-rennes1.fr/odameron/debugVirtuoso/>.
:display :startRelation :posStart.
:display :stopRelation :posStop.
""")
for i in range(nbGenes):
geneIdent = ":gene" + str(i)
dataFile.write("\n" + geneIdent + " rdf:type :Gene.\n")
posStart = random.randint(1, chromosomeLength-geneLengthMax)
posStop = posStart + random.randint(1, geneLengthMax)
dataFile.write(geneIdent + " :posStart \"" + str(posStart) +
"\"^^xsd:numeric.\n")
dataFile.write(geneIdent + " :posStop \"" + str(posStop) +
"\"^^xsd:numeric.\n")
===== getOverlap.sparql
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX : <http://www.univ-rennes1.fr/odameron/debugVirtuoso/>
SELECT (count(*) as ?nbOverlap)
WHERE {
?gene1 a :Gene;
:posStart ?start1;
:posStop ?stop1.
?gene2 a :Gene;
:posStart ?start2;
:posStop ?stop2.
FILTER (?start1 < ?start2 && ?start1 < ?stop2 && ?start2 < ?stop1)
}
===== getOverlapSLOW.sparql
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX : <http://www.univ-rennes1.fr/odameron/debugVirtuoso/>
SELECT (count(*) as ?nbOverlap)
WHERE {
:display :startRelation ?startRel.
:display :stopRelation ?stopRel.
?gene1 a :Gene;
?startRel ?start1;
?stopRel ?stop1.
?gene2 a :Gene;
?startRel ?start2;
?stopRel ?stop2.
FILTER (?start1 < ?start2 && ?start1 < ?stop2 && ?start2 < ?stop1)
}
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