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Commit b66689ef authored by Patrick Meidl's avatar Patrick Meidl
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fixed sql bug in fetch_by_transcript_archive_id()

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modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+ 1
− 0
View file @ b66689ef
......@@ -319,6 +319,7 @@ sub fetch_by_transcript_archive_id {
FROM gene_archive ga, mapping_session m
WHERE ga.transcript_stable_id = ?
AND ga.transcript_version = ?
AND ga.mapping_session_id = m.mapping_session_id
);
my $sth = $self->prepare( $sql );
......
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+ 55
− 38
View file @ b66689ef
......@@ -113,7 +113,6 @@ sub fetch_by_dbID {
}
=head2 fetch_by_db_accession
Arg [1] : string $dbname - The name of the database which the provided
......@@ -471,7 +470,6 @@ sub exists {
}
=head2 fetch_all_by_Gene
Arg [1] : Bio::EnsEMBL::Gene $gene
......@@ -812,7 +810,7 @@ sub _fetch_by_object_type {
sub list_gene_ids_by_extids{
my ($self,$name) = @_;
my %T = map { ($_,1) }
my %T = map { ($_, 1) }
$self->_type_by_external_id( $name, 'Translation', 'gene' ),
$self->_type_by_external_id( $name, 'Transcript', 'gene' ),
$self->_type_by_external_id( $name, 'Gene' );
......@@ -820,7 +818,6 @@ sub list_gene_ids_by_extids{
}
=head2 list_transcript_ids_by_extids
Arg [1] : string $external_id
......@@ -839,7 +836,7 @@ sub list_transcript_ids_by_extids{
my ($self,$name) = @_;
my @transcripts;
my %T = map { ($_,1) }
my %T = map { ($_, 1) }
$self->_type_by_external_id( $name, 'Translation', 'transcript' ),
$self->_type_by_external_id( $name, 'Transcript' );
return keys %T;
......@@ -860,63 +857,82 @@ sub list_transcript_ids_by_extids{
sub list_translation_ids_by_extids{
my ($self,$name) = @_;
return $self->_type_by_external_id( $name, 'Translation' );
return $self->_type_by_external_id($name, 'Translation');
}
=head2 _type_by_external_id
Arg [1] : string $name
(dbprimary_acc)
Arg [2] : string $ensType
(Object_type)
Arg [3] : string $extraType
(other object type to be returned) - optional
Example : $self->_type_by_external_id( $name, 'Translation' )
Arg [1] : string $name - dbprimary_acc
Arg [2] : string $ensType - ensembl_object_type
Arg [3] : (optional) string $extraType
other object type to be returned
Example : $self->_type_by_external_id($name, 'Translation');
Description: Gets
Returntype : list of ensembl_IDs
Returntype : list of dbIDs (gene_id, transcript_id, etc.)
Exceptions : none
Caller : list_translation_ids_by_extids
translationids_by_extids
geneids_by_extids
geneids_by_extids
Status : Stable
=cut
sub _type_by_external_id{
my ($self,$name,$ensType,$extraType) = @_;
my ($self, $name, $ensType, $extraType) = @_;
my $from_sql = '';
my $where_sql = '';
my $ID_sql = "oxr.ensembl_id";
if(defined $extraType) {
if(lc($extraType) eq 'translation') {
if (defined $extraType) {
if (lc($extraType) eq 'translation') {
$ID_sql = "tl.translation_id";
} else {
$ID_sql = "t.${extraType}_id";
}
if(lc($ensType) eq 'translation') {
$from_sql = 'transcript as t, translation as tl, ';
$where_sql = 't.transcript_id = tl.transcript_id and ' .
'tl.translation_id = oxr.ensembl_id and ';
if (lc($ensType) eq 'translation') {
$from_sql = 'transcript t, translation tl, ';
$where_sql = qq(
t.transcript_id = tl.transcript_id AND
tl.translation_id = oxr.ensembl_id AND
t.is_current = 1 AND
);
} else {
$from_sql = 'transcript as t, ';
$where_sql = 't.'.lc($ensType).'_id = oxr.ensembl_id and ';
$from_sql = 'transcript t, ';
$where_sql = 't.'.lc($ensType).'_id = oxr.ensembl_id AND '.
't.is_current = 1 AND ';
}
}
if (lc($ensType) eq 'gene') {
$from_sql = 'gene g, ';
$where_sql = 'g.gene_id = oxr.ensembl_id AND g.is_current = 1 AND ';
} elsif (lc($ensType) eq 'transcript') {
$from_sql = 'transcript t, ';
$where_sql = 't.transcript_id = oxr.ensembl_id AND t.is_current = 1 AND ';
} elsif (lc($ensType) eq 'translation') {
$from_sql = 'transcript t, translation tl, ';
$where_sql = qq(
t.transcript_id = tl.transcript_id AND
tl.translation_id = oxr.ensembl_id AND
t.is_current = 1 AND
);
}
my @queries = (
"select $ID_sql
from $from_sql xref, object_xref as oxr
where $where_sql xref.dbprimary_acc = ? and
xref.xref_id = oxr.xref_id and oxr.ensembl_object_type= ?",
"select $ID_sql
from $from_sql xref, object_xref as oxr
where $where_sql xref.display_label = ? and
xref.xref_id = oxr.xref_id and oxr.ensembl_object_type= ?",
"select $ID_sql
from $from_sql object_xref as oxr, external_synonym as syn
where $where_sql syn.synonym = ? and
syn.xref_id = oxr.xref_id and oxr.ensembl_object_type= ?",
"SELECT $ID_sql
FROM $from_sql xref x, object_xref oxr
WHERE $where_sql x.dbprimary_acc = ? AND
x.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
"SELECT $ID_sql
FROM $from_sql xref x, object_xref oxr
WHERE $where_sql x.display_label = ? AND
x.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
"SELECT $ID_sql
FROM $from_sql object_xref oxr, external_synonym syn
WHERE $where_sql syn.synonym = ? AND
syn.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
);
# Increase speed of query by splitting the OR in query into three separate
......@@ -929,8 +945,8 @@ sub _type_by_external_id{
foreach( @queries ) {
my $sth = $self->prepare( $_ );
$sth->bind_param(1,"$name",SQL_VARCHAR);
$sth->bind_param(2,$ensType,SQL_VARCHAR);
$sth->bind_param(1, $name, SQL_VARCHAR);
$sth->bind_param(2, $ensType, SQL_VARCHAR);
$sth->execute();
while( my $r = $sth->fetchrow_array() ) {
if( !exists $hash{$r} ) {
......@@ -942,6 +958,7 @@ sub _type_by_external_id{
return @result;
}
=head2 fetch_all_by_description
Arg [1] : string description to search for. Include % etc in this string
......
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+ 77
− 63
View file @ b66689ef
package Bio::EnsEMBL::DBSQL::ExonAdaptor;
#EnsEMBL Exon reading writing adaptor for mySQL
#
# Copyright EMBL-EBI 2001
......@@ -33,20 +35,16 @@ Post questions/comments to the Ensembl dev list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::DBSQL::ExonAdaptor;
use vars qw( @ISA );
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
use vars qw( @ISA );
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
#_tables
#
# Arg [1] : none
......@@ -82,22 +80,18 @@ sub _columns {
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
return ( 'e.exon_id', 'e.seq_region_id', 'e.seq_region_start' ,'e.seq_region_end',
'e.seq_region_strand', 'e.phase','e.end_phase',
'esi.stable_id', 'esi.version',$created_date,
$modified_date );
# esi.stable_id esi.version UNIX_TIMESTAMP(created_date)
# UNIX_TIMESTAMP(modified_date) );
return ( 'e.exon_id', 'e.seq_region_id', 'e.seq_region_start',
'e.seq_region_end', 'e.seq_region_strand', 'e.phase','e.end_phase',
'e.is_current',
'esi.stable_id', 'esi.version', $created_date, $modified_date );
}
sub _left_join {
return ( [ 'exon_stable_id', "esi.exon_id = e.exon_id" ]);
}
# _final_clause
#
# Arg [1] : none
......@@ -114,14 +108,13 @@ sub _final_clause {
}
=head2 fetch_by_stable_id
Arg [1] : string $stable_id
the stable id of the exon to retrieve
Example : $exon = $exon_adaptor->fetch_by_stable_id('ENSE0000988221');
Description: Retrieves an Exon from the database via its stable id
Returntype : Bio::EnsEMBL::Exon in contig coordinates
Returntype : Bio::EnsEMBL::Exon in native coordinates.
Exceptions : none
Caller : general
Status : Stable
......@@ -129,16 +122,36 @@ sub _final_clause {
=cut
sub fetch_by_stable_id {
my ( $self, $stable_id ) = @_;
my ($self, $stable_id) = @_;
my $constraint = "esi.stable_id = '$stable_id' AND e.is_current = 1";
my ($exon) = @{ $self->generic_fetch($constraint) };
return $exon;
}
my $constraint = "esi.stable_id = \"$stable_id\"";
=head2 fetch_all_versions_by_stable_id
# should be only one :-)
my $exons = $self->SUPER::generic_fetch( $constraint );
Arg [1] : String $stable_id
The stable ID of the exon to retrieve
Example : my $exon = $exon_adaptor->fetch_all_version_by_stable_id
('ENSE00000309301');
Description : Similar to fetch_by_stable_id, but retrieves all versions of an
exon stored in the database.
Returntype : listref of Bio::EnsEMBL::Exon objects
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : At Risk
=cut
if( ! @$exons ) { return undef }
sub fetch_all_versions_by_stable_id {
my ($self, $stable_id) = @_;
return $exons->[0];
my $constraint = "esi.stable_id = '$stable_id'";
return $self->generic_fetch($constraint);
}
......@@ -175,14 +188,13 @@ sub fetch_all_by_Transcript {
$self->{'tables'} = \@tables;
$self->{'final_clause'} = "ORDER BY et.transcript_id, et.rank";
my $constraint = "et.transcript_id = ".$transcript->dbID() .
" AND e.exon_id = et.exon_id";
# fetch all of the exons
my $exons = $self->fetch_all_by_Slice_constraint($slice,$constraint);
my $exons = $self->fetch_all_by_Slice_constraint($slice, $constraint);
#un-override the table definition
# un-override the table definition
$self->{'tables'} = undef;
$self->{'final_clause'} = undef;
......@@ -199,7 +211,6 @@ sub fetch_all_by_Transcript {
}
=head2 store
Arg [1] : Bio::EnsEMBL::Exon $exon
......@@ -216,7 +227,7 @@ sub fetch_all_by_Transcript {
=cut
sub store {
my ( $self, $exon ) = @_;
my ($self, $exon) = @_;
if( ! $exon->isa('Bio::EnsEMBL::Exon') ) {
throw("$exon is not a EnsEMBL exon - not storing.");
......@@ -233,11 +244,15 @@ sub store {
throw("Exon does not have all attributes to store");
}
# default to is_current = 1 if this attribute is not set
my $is_current = $exon->is_current;
$is_current = 1 unless (defined($is_current));
my $exon_sql = q{
INSERT into exon ( seq_region_id, seq_region_start,
seq_region_end, seq_region_strand, phase,
end_phase )
VALUES ( ?, ?, ?, ?, ?, ? )
end_phase, is_current )
VALUES ( ?, ?, ?, ?, ?, ?, ? )
};
my $exonst = $self->prepare($exon_sql);
......@@ -249,12 +264,13 @@ sub store {
($exon, $seq_region_id) = $self->_pre_store($exon);
#store the exon
$exonst->bind_param(1,$seq_region_id, SQL_INTEGER);
$exonst->bind_param(2,$exon->start, SQL_INTEGER);
$exonst->bind_param(3,$exon->end, SQL_INTEGER);
$exonst->bind_param(4,$exon->strand, SQL_TINYINT);
$exonst->bind_param(5,$exon->phase, SQL_TINYINT);
$exonst->bind_param(6,$exon->end_phase, SQL_TINYINT);
$exonst->bind_param(1, $seq_region_id, SQL_INTEGER);
$exonst->bind_param(2, $exon->start, SQL_INTEGER);
$exonst->bind_param(3, $exon->end, SQL_INTEGER);
$exonst->bind_param(4, $exon->strand, SQL_TINYINT);
$exonst->bind_param(5, $exon->phase, SQL_TINYINT);
$exonst->bind_param(6, $exon->end_phase, SQL_TINYINT);
$exonst->bind_param(7, $is_current, SQL_TINYINT);
$exonst->execute();
$exonId = $exonst->{'mysql_insertid'};
......@@ -268,18 +284,10 @@ sub store {
"stable_id = ?, " .
"exon_id = ?, ";
$statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($exon->created_date()) . ",";
# if( $exon->created_date() ) {
# $statement .= "created_date = from_unixtime( ".$exon->created_date()."),";
# } else {
# $statement .= "created_date = \"0000-00-00 00:00:00\",";
# }
$statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($exon->modified_date()) ;
# if( $exon->modified_date() ) {
# $statement .= "modified_date = from_unixtime( ".$exon->modified_date().")";
# } else {
# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
# }
$statement .= "created_date = " .
$self->db->dbc->from_seconds_to_date($exon->created_date()) . ",";
$statement .= "modified_date = " .
$self->db->dbc->from_seconds_to_date($exon->modified_date()) ;
my $sth = $self->prepare( $statement );
......@@ -319,9 +327,9 @@ sub store {
next;
}
$sf_sth->bind_param(1,$exonId,SQL_INTEGER);
$sf_sth->bind_param(2,$sf->dbID,SQL_INTEGER);
$sf_sth->bind_param(3,$type,SQL_VARCHAR);
$sf_sth->bind_param(1, $exonId, SQL_INTEGER);
$sf_sth->bind_param(2, $sf->dbID, SQL_INTEGER);
$sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
......@@ -382,7 +390,7 @@ sub remove {
my $sth = $self->prepare("SELECT feature_type, feature_id " .
"FROM supporting_feature " .
"WHERE exon_id = ?");
$sth->bind_param(1,$exon->dbID,SQL_INTEGER);
$sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
while(my ($type, $feature_id) = $sth->fetchrow()){
......@@ -403,21 +411,21 @@ sub remove {
# delete the association to supporting features
$sth = $self->prepare("DELETE FROM supporting_feature WHERE exon_id = ?");
$sth->bind_param(1,$exon->dbID,SQL_INTEGER);
$sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
# delete the exon stable identifier
$sth = $self->prepare( "DELETE FROM exon_stable_id WHERE exon_id = ?" );
$sth->bind_param(1,$exon->dbID,SQL_INTEGER);
$sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
# delete the exon
$sth = $self->prepare( "DELETE FROM exon WHERE exon_id = ?" );
$sth->bind_param(1,$exon->dbID,SQL_INTEGER);
$sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
......@@ -446,6 +454,7 @@ sub list_dbIDs {
return $self->_list_dbIDs("exon");
}
=head2 list_stable_ids
Arg [1] : none
......@@ -492,14 +501,13 @@ sub _objs_from_sth {
my ( $exon_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $phase,
$end_phase, $stable_id, $version, $created_date,
$end_phase, $is_current, $stable_id, $version, $created_date,
$modified_date );
$sth->bind_columns( \$exon_id, \$seq_region_id,
\$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$phase,
\$end_phase, \$stable_id, \$version, \$created_date,
\$modified_date );
$sth->bind_columns( \$exon_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$phase,
\$end_phase, \$is_current, \$stable_id, \$version,
\$created_date, \$modified_date );
my $asm_cs;
my $cmp_cs;
......@@ -611,8 +619,8 @@ sub _objs_from_sth {
}
#finally, create the new repeat feature
push @exons, Bio::EnsEMBL::Exon->new
( '-start' => $seq_region_start,
push @exons, Bio::EnsEMBL::Exon->new(
'-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
'-adaptor' => $self,
......@@ -623,7 +631,9 @@ sub _objs_from_sth {
'-created_date' => $created_date || undef,
'-modified_date' => $modified_date || undef,
'-phase' => $phase,
'-end_phase' => $end_phase )
'-end_phase' => $end_phase,
'is_current' => $is_current
);
}
......@@ -663,7 +673,7 @@ sub get_stable_entry_info {
FROM exon_stable_id
WHERE exon_id = ");
$sth->bind_param(1,$exon->dbID,SQL_INTEGER);
$sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
# my @array = $sth->fetchrow_array();
......@@ -677,6 +687,7 @@ sub get_stable_entry_info {
return 1;
}
=head2 fetch_all_by_gene_id
Description: DEPRECATED. This method should not be needed - Exons can
......@@ -695,7 +706,9 @@ sub fetch_all_by_gene_id {
if( !$gene_id ) {
$self->throw("Gene dbID not defined");
}
$self->{rchash} = {};
my $query = qq {
SELECT
STRAIGHT_JOIN
......@@ -740,3 +753,4 @@ sub fetch_all_by_gene_id {
1;
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+ 495
− 470
View file @ b66689ef
This diff is collapsed.
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 393
− 353
View file @ b66689ef
This diff is collapsed.
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