[Bioperl-l] bioperl-db: posqgresql adaptor
Tim Henderson
tjh@alodar.com
Tue, 19 Nov 2002 11:23:27 -0800
I believe this same bug exists in the mysql adaptor. It doesn't cause an
exception to be thrown, but it does cause DBD::mysql::st to print a
warning message when bind_param() fails. See the debug output below.
-- Tim
[tjh@feature tjh]$ bin/fetch_by_accession.pl --debug=2 X92703
attempting to load adaptor class for Bio::SeqI
attempting to load module Bio::DB::BioSQL::SeqIAdaptor
attempting to load module Bio::DB::BioSQL::SeqAdaptor
instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
attempting to load adaptor class for BioNamespace
attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor
instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::SeqAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::PrimarySeqAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::SeqAdaptor
preparing UK select statement: SELECT bioentry.bioentry_id,
bioentry.display_id, bioentry.identifier, bioentry.accession,
bioentry.description, bioentry.entry_version, bioentry.biodatabase_id,
bioentry.taxon_id FROM bioentry WHERE entry_version = ? AND accession = ?
SeqAdaptor: binding UK column 1 to "0" (version)
SeqAdaptor: binding UK column 2 to "X92703" (accession_number)
attempting to load adaptor class for Bio::PrimarySeq
attempting to load module Bio::DB::BioSQL::PrimarySeqAdaptor
instantiating adaptor class Bio::DB::BioSQL::PrimarySeqAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BioNamespaceAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::BioNamespaceAdaptor
preparing PK select statement: SELECT biodatabase.biodatabase_id,
biodatabase.name, biodatabase.authority FROM biodatabase WHERE
biodatabase_id = ?
BioNamespaceAdaptor: binding PK column to "1"
attempting to load adaptor class for Bio::Species
attempting to load module Bio::DB::BioSQL::SpeciesAdaptor
instantiating adaptor class Bio::DB::BioSQL::SpeciesAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::SpeciesAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::SpeciesAdaptor
preparing PK select statement: SELECT taxon.taxon_id, taxon.common_name,
taxon.full_lineage, taxon.ncbi_taxon_id, taxon.binomial, taxon.variant
FROM taxon WHERE taxon_id = ?
SpeciesAdaptor: binding PK column to "2"
attempting to load adaptor class for Biosequence
attempting to load module Bio::DB::BioSQL::BiosequenceAdaptor
instantiating adaptor class Bio::DB::BioSQL::BiosequenceAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BiosequenceAdaptor
Using Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver as driver peer
for Bio::DB::BioSQL::BiosequenceAdaptor
preparing UK select statement: SELECT biosequence.bioentry_id,
biosequence.seq_version, biosequence.division, biosequence.seq_length,
biosequence.alphabet, NULL, biosequence.bioentry_id FROM biosequence
WHERE bioentry_id = ?
BiosequenceAdaptor: binding UK column 1 to "7" (primary_seq)
attempting to load adaptor class for Bio::AnnotationCollectionI
attempting to load module
Bio::DB::BioSQL::AnnotationCollectionIAdaptor
attempting to load module
Bio::DB::BioSQL::AnnotationCollectionAdaptor
instantiating adaptor class Bio::DB::BioSQL::AnnotationCollectionAdaptor
attempting to load adaptor class for Bio::Annotation::Reference
attempting to load module Bio::DB::BioSQL::ReferenceAdaptor
instantiating adaptor class Bio::DB::BioSQL::ReferenceAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::ReferenceAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::ReferenceAdaptor
preparing SELECT ASSOC query: SELECT t2.reference_id,
t2.reference_authors, t2.reference_title, t2.reference_location,
t2.reference_medline, bioentry_reference.reference_start,
bioentry_reference.reference_end FROM bioentry t1, reference t2,
bioentry_reference WHERE t1.bioentry_id = bioentry_reference.bioentry_id
AND t2.reference_id = bioentry_reference.reference_id AND t1.bioentry_id = ?
ReferenceAdaptor: binding ASSOC column 1 to "7" (FK to Bio::Seq)
attempting to load adaptor class for Bio::Annotation::OntologyTerm
attempting to load module Bio::DB::BioSQL::OntologyTermAdaptor
attempting to load adaptor class for Bio::Root::Root
attempting to load module Bio::DB::BioSQL::RootAdaptor
attempting to load adaptor class for Bio::Root::RootI
attempting to load module Bio::DB::BioSQL::RootIAdaptor
attempting to load module Bio::DB::BioSQL::RootAdaptor
attempting to load adaptor class for Bio::AnnotationI
attempting to load module Bio::DB::BioSQL::AnnotationIAdaptor
attempting to load module Bio::DB::BioSQL::AnnotationAdaptor
attempting to load adaptor class for Bio::Ontology::TermI
attempting to load module Bio::DB::BioSQL::TermIAdaptor
attempting to load module Bio::DB::BioSQL::TermAdaptor
instantiating adaptor class Bio::DB::BioSQL::TermAdaptor
attempting to load adaptor class for Bio::Ontology::Term
attempting to load module Bio::DB::BioSQL::TermAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::TermAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::TermAdaptor
preparing UK select statement: SELECT ontology_term.ontology_term_id,
ontology_term.term_identifier, ontology_term.term_name,
ontology_term.term_definition, ontology_term.category_id FROM
ontology_term WHERE term_name = ?
TermAdaptor: binding UK column 1 to "Annotation Tags" (name)
preparing SELECT ASSOC query: SELECT t2.ontology_term_id,
t2.term_identifier, t2.term_name, t2.term_definition, t2.category_id
FROM bioentry t1, ontology_term t2, bioentry_qualifier_value WHERE
t1.bioentry_id = bioentry_qualifier_value.bioentry_id AND
t2.ontology_term_id = bioentry_qualifier_value.ontology_term_id AND
(t1.bioentry_id = ? AND t2.category_id != ?)
TermAdaptor: binding ASSOC column 1 to "7" (FK to Bio::Seq)
TermAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::OntologyTerm::category)
attempting to load adaptor class for Bio::Annotation::SimpleValue
attempting to load module Bio::DB::BioSQL::SimpleValueAdaptor
instantiating adaptor class Bio::DB::BioSQL::SimpleValueAdaptor
attempting to load adaptor class for Bio::Ontology::Term
attempting to load module Bio::DB::BioSQL::TermAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::SimpleValueAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::TermAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::SimpleValueAdaptor
preparing SELECT ASSOC query: SELECT t2.ontology_term_id, t2.term_name,
bioentry_qualifier_value.qualifier_value, t2.category_id FROM bioentry
t1, ontology_term t2, bioentry_qualifier_value WHERE t1.bioentry_id =
bioentry_qualifier_value.bioentry_id AND t2.ontology_term_id =
bioentry_qualifier_value.ontology_term_id AND (t1.bioentry_id = ? AND
t2.category_id = ?)
SimpleValueAdaptor: binding ASSOC column 1 to "7" (FK to Bio::Seq)
SimpleValueAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::SimpleValue::category)
attempting to load adaptor class for Bio::Annotation::DBLink
attempting to load module Bio::DB::BioSQL::DBLinkAdaptor
instantiating adaptor class Bio::DB::BioSQL::DBLinkAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::DBLinkAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::DBLinkAdaptor
preparing SELECT ASSOC query: SELECT t2.dbxref_id, t2.dbname,
t2.accession, t2.version FROM bioentry t1, dbxref t2, bioentry_dblink
WHERE t1.bioentry_id = bioentry_dblink.bioentry_id AND t2.dbxref_id =
bioentry_dblink.dbxref_id AND t1.bioentry_id = ?
DBLinkAdaptor: binding ASSOC column 1 to "7" (FK to Bio::Seq)
attempting to load adaptor class for Bio::Annotation::Comment
attempting to load module Bio::DB::BioSQL::CommentAdaptor
instantiating adaptor class Bio::DB::BioSQL::CommentAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::CommentAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::CommentAdaptor
preparing query: SELECT t1.comment_id, t1.comment_text, t1.comment_rank,
t1.bioentry_id FROM comment t1 WHERE t1.bioentry_id = ?
Query FIND Bio::Annotation::Comment BY Bio::Seq: binding column 1 to "7"
attempting to load adaptor class for Bio::SeqFeatureI
attempting to load module Bio::DB::BioSQL::SeqFeatureIAdaptor
attempting to load module Bio::DB::BioSQL::SeqFeatureAdaptor
instantiating adaptor class Bio::DB::BioSQL::SeqFeatureAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::SeqFeatureAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::SeqFeatureAdaptor
preparing query: SELECT t1.seqfeature_id, NULL, t1.seqfeature_rank,
t1.bioentry_id, t1.ontology_term_id, t1.seqfeature_source_id FROM
seqfeature t1 WHERE t1.bioentry_id = ?
Query FIND FEATURE BY SEQ: binding column 1 to "7"
preparing PK select statement: SELECT ontology_term.ontology_term_id,
ontology_term.term_identifier, ontology_term.term_name,
ontology_term.term_definition, ontology_term.category_id FROM
ontology_term WHERE ontology_term_id = ?
TermAdaptor: binding PK column to "2"
TermAdaptor: binding PK column to "1"
TermAdaptor: binding PK column to "4"
TermAdaptor: binding PK column to "3"
attempting to load adaptor class for Bio::LocationI
attempting to load module Bio::DB::BioSQL::LocationIAdaptor
attempting to load module Bio::DB::BioSQL::LocationAdaptor
instantiating adaptor class Bio::DB::BioSQL::LocationAdaptor
attempting to load driver for adaptor class Bio::DB::BioSQL::LocationAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver
peer for Bio::DB::BioSQL::LocationAdaptor
preparing query: SELECT t1.seqfeature_location_id, t1.seq_start,
t1.seq_end, t1.seq_strand, t1.location_rank, t1.seqfeature_id,
t1.dbxref_id FROM seqfeature_location t1 WHERE t1.seqfeature_id = ?
Query FIND LOCATION BY FEATURE: binding column 1 to "18"
preparing SELECT ASSOC query: SELECT t2.ontology_term_id,
t2.term_identifier, t2.term_name, t2.term_definition, t2.category_id
FROM seqfeature t1, ontology_term t2, seqfeature_qualifier_value WHERE
t1.seqfeature_id = seqfeature_qualifier_value.seqfeature_id AND
t2.ontology_term_id = seqfeature_qualifier_value.ontology_term_id AND
(t1.seqfeature_id = ? AND t2.category_id != ?)
TermAdaptor: binding ASSOC column 1 to "18" (FK to Bio::SeqFeature::Generic)
TermAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::OntologyTerm::category)
preparing SELECT ASSOC query: SELECT t2.ontology_term_id, t2.term_name,
seqfeature_qualifier_value.qualifier_value, t2.category_id FROM
seqfeature t1, ontology_term t2, seqfeature_qualifier_value WHERE
t1.seqfeature_id = seqfeature_qualifier_value.seqfeature_id AND
t2.ontology_term_id = seqfeature_qualifier_value.ontology_term_id AND
(t1.seqfeature_id = ? AND t2.category_id = ?)
SimpleValueAdaptor: binding ASSOC column 1 to "18" (FK to
Bio::SeqFeature::Generic)
SimpleValueAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::SimpleValue::category)
preparing query: SELECT t1.comment_id, t1.comment_text, t1.comment_rank,
t1.bioentry_id FROM comment t1 WHERE 1 = 1
Query FIND Bio::Annotation::Comment BY Bio::SeqFeature::Generic: binding
column 1 to "18"
DBD::mysql::st bind_param failed: Illegal parameter number at
/home/tjh/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
line 938.
TermAdaptor: binding PK column to "10"
Query FIND LOCATION BY FEATURE: binding column 1 to "20"
TermAdaptor: binding ASSOC column 1 to "20" (FK to Bio::SeqFeature::Generic)
TermAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::OntologyTerm::category)
SimpleValueAdaptor: binding ASSOC column 1 to "20" (FK to
Bio::SeqFeature::Generic)
SimpleValueAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::SimpleValue::category)
TermAdaptor: binding PK column to "13"
Query FIND LOCATION BY FEATURE: binding column 1 to "19"
TermAdaptor: binding ASSOC column 1 to "19" (FK to Bio::SeqFeature::Generic)
TermAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::OntologyTerm::category)
SimpleValueAdaptor: binding ASSOC column 1 to "19" (FK to
Bio::SeqFeature::Generic)
SimpleValueAdaptor: binding ASSOC column 2 to "5" (constraint
Bio::Annotation::SimpleValue::category)
preparing SELECT statement: SELECT biosequence_str FROM biosequence
WHERE bioentry_id = ?
<<snip>>