openlink
sparql query with BIND giving "SR319: Max row length is exceeded when trying to store a string of 52 chars into a temp col"
Dear Hugh, Dear all,
I observe an SR319 with the following query:
PREFIX up:http://purl.uniprot.org/core/ PREFIX keywords:http://purl.uniprot.org/keywords/ PREFIX uniprotkb:http://purl.uniprot.org/uniprot/ PREFIX taxon:http://purl.uniprot.org/taxonomy/ PREFIX ec:http://purl.uniprot.org/enzyme/ PREFIX rdf:http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX rdfs:http://www.w3.org/2000/01/rdf-schema# PREFIX skos:http://www.w3.org/2004/02/skos/core# PREFIX owl:http://www.w3.org/2002/07/owl# PREFIX bibo:http://purl.org/ontology/bibo/ PREFIX dc:http://purl.org/dc/terms/ PREFIX xsd:http://www.w3.org/2001/XMLSchema# PREFIX faldo:http://biohackathon.org/resource/faldo# SELECT ?protein ?proteome WHERE { ?protein a up:Sequence . ?protein up:sequenceFor ?member . ?member up:proteome ?proteomeComponent . BIND(IRI(STRBEFORE(STR(?proteomeComponent), "#")) AS ?proteome) } GROUP BY ?protein ?proteome HAVING (COUNT(?proteome) > 1);
The dataset is uniprot. This happens on both 2015_03 and 2015_04 versions. Virtuoso is virtuoso-opensource tags/v7.2.0.1
Here are the details on the 2015_04 dataset. SR319 comes after ~3 minutes:
[user@testmachine1 ~]$ ~/bin/isql -H localhost:1112
[...]
SQL> trace_on();
Done. -- 0 msec.
SQL> sparql PREFIX up:http://purl.uniprot.org/core/ PREFIX keywords:http://purl.uniprot.org/keywords/ PREFIX uniprotkb:http://purl.uniprot.org/uniprot/ PREFIX taxon:http://purl.uniprot.org/taxonomy/ PREFIX ec:http://purl.uniprot.org/enzyme/ PREFIX rdf:http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX rdfs:http://www.w3.org/2000/01/rdf-schema# PREFIX skos:http://www.w3.org/2004/02/skos/core# PREFIX owl:http://www.w3.org/2002/07/owl# PREFIX bibo:http://purl.org/ontology/bibo/ PREFIX dc:http://purl.org/dc/terms/ PREFIX xsd:http://www.w3.org/2001/XMLSchema# PREFIX faldo:http://biohackathon.org/resource/faldo# SELECT ?protein ?proteome WHERE { ?protein a up:Sequence . ?protein up:sequenceFor ?member . ?member up:proteome ?proteomeComponent . BIND(IRI(STRBEFORE(STR(?proteomeComponent), "#")) AS ?proteome) } GROUP BY ?protein ?proteome HAVING (COUNT(?proteome) > 1);
**\* Error 22026: [Virtuoso Driver][Virtuoso Server]SR319: Max row length is exceeded when trying to store a string of 52 chars into a temp col
at line 6 of Top-Level:
sparql PREFIX up:http://purl.uniprot.org/core/ PREFIX keywords:http://purl.uniprot.org/keywords/ PREFIX uniprotkb:http://purl.uniprot.org/uniprot/ PREFIX taxon:http://purl.uniprot.org/taxonomy/ PREFIX ec:http://purl.uniprot.org/enzyme/ PREFIX rdf:http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX rdfs:http://www.w3.org/2000/01/rdf-schema# PREFIX skos:http://www.w3.org/2004/02/skos/core# PREFIX owl:http://www.w3.org/2002/07/owl# PREFIX bibo:http://purl.org/ontology/bibo/ PREFIX dc:http://purl.org/dc/terms/ PREFIX xsd:http://www.w3.org/2001/XMLSchema# PREFIX faldo:http://biohackathon.org/resource/faldo# SELECT ?protein ?proteome WHERE { ?protein a up:Sequence . ?protein up:sequenceFor ?member . ?member up:proteome ?proteomeComponent . BIND(IRI(STRBEFORE(STR(?proteomeComponent), "#")) AS ?proteome) } GROUP BY ?protein ?proteome HAVING (COUNT(?proteome) > 1)
SQL>
logs with trace_on():
user@testmachine1 ~]$ tail -f /[logspath]/2015_04.1/run.log
[...]
10:55:43 LTRS_1 dba 127.0.0.1 1112:57 Commit transact 0x7f73084b57b0 0
10:55:43 LTRS_2 dba 127.0.0.1 1112:57 Restart transact 0x7f73084b57b0
10:55:52 CSLQ_0 dba 127.0.0.1 1112:57 s1112_57_0 sparql PREFIX up:http://purl.uniprot.org/core/ PREFIX keywords:http://purl.uniprot.org/keywords/ PREFIX uniprotkb:http://purl.uniprot.org/uniprot/ PREFIX taxon:http://purl.uniprot.org/taxonomy/ PREFIX ec:http://purl.uniprot.org/enzyme/ PREFIX rdf:http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX rdfs:http://www.w3.org/2000/01/rdf-schema# PREFIX skos:http://www.w3.org/2004/02/skos/core# PREFIX owl:http://www.w3.org/2002/07/owl# PREFIX bibo:http://purl.org/ontology/bibo/ PREF
10:55:52 EXEC_1 dba 127.0.0.1 1112:57 s1112_57_0 Exec 1 time(s) sparql PREFIX up:http://purl.uniprot.org/core/ PREFIX keywords:http://purl.uniprot.org/keywords/ PREFIX uniprotkb:http://purl.uniprot.org/uniprot/ PREFIX taxon:http://purl.uniprot.org/taxonomy/ PREFIX ec:http://purl.uniprot.org/enzyme/ PREFIX rdf:http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX rdfs:http://www.w3.org/2000/01/rdf-schema# PREFIX skos:http://www.w3.org/2004/02/skos/core# PREFIX owl:http://www.w3.org/2002/07/owl# PREFIX bibo:http://purl.org/ontology/bibo/ PREFI
10:55:58 LTRS_0 dba Internal Internal Begin transact 0x7f7300003490
10:55:58 LTRS_1 dba Internal Internal Commit transact 0x7f7300003490 120259084288
10:55:58 LTRS_2 dba Internal Internal Restart transact 0x7f7300003490
10:55:58 LTRS_1 dba Internal Internal Commit transact 0x7f7300003490 64424509440
10:55:58 LTRS_2 dba Internal Internal Restart transact 0x7f7300003490
10:55:58 LTRS_1 dba Internal Internal Commit transact 0x7f7300003490 120259084288
10:55:58 LTRS_2 dba Internal Internal Restart transact 0x7f7300003490
10:55:58 LTRS_1 dba Internal Internal Commit transact 0x7f7300003490 0
10:55:58 LTRS_2 dba Internal Internal Restart transact 0x7f7300003490
10:55:58 LTRS_1 dba Internal Internal Commit transact 0x7f7300003490 0
10:55:58 LTRS_2 dba Internal Internal Restart transact 0x7f7300003490
10:58:30 ERRS_0 22026 SR319 Max row length is exceeded when trying to store a string of 52 chars into a temp col
10:58:30 LTRS_1 dba 127.0.0.1 1112:57 Commit transact 0x7f73084b57b0 140131897966592
10:58:30 LTRS_2 dba 127.0.0.1 1112:57 Restart transact 0x7f73084b57b0
I can see that similar issues have been reported in:
- https://github.com/openlink/virtuoso-opensource/issues/118
- https://github.com/openlink/virtuoso-opensource/issues/93
Thanks for your help!
(int. ref. UPS-96)
I have been able to recreate this against the uniprot live sparql endpoint http://beta.sparql.uniprot.org/sparql/, and reported it to development. In the short term, the query will probably need to be restructured to avoid this limit on the temp table col size...
