Skip to content
Snippets Groups Projects
Commit 69bacbf3 authored by Graham McVicker's avatar Graham McVicker
Browse files

DBEntryAdaptor::store changed so can no longer add external_db entries and refactored a bit

parent 38b174bd
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+ 95
− 158
View file @ 69bacbf3
......@@ -19,10 +19,7 @@ $dbEntry = $db_entry_adaptor->fetch_by_dbID($id);
=head1 CONTACT
Arne Stabenau: stabenau@ebi.ac.uk
Ewan Birney : birney@ebi.ac.uk
=head1 APPENDIX
Post questions to the EnsEMBL developer list <ensembl-dev@ebi.ac.uk>
=cut
......@@ -110,182 +107,122 @@ sub fetch_by_dbID {
sub store {
my ( $self, $exObj, $ensObject, $ensType ) = @_;
my $dbJustInserted;
my ( $self, $exObj, $ensObject, $ensType ) = @_;
my $dbJustInserted;
# check if db exists
# urlPattern dbname release
my $sth = $self->prepare( "
#
# Check for the existance of the external_db, throw if it does not exist
#
my $sth = $self->prepare( "
SELECT external_db_id
FROM external_db
WHERE db_name = ?
AND release = ?
" );
$sth->execute( $exObj->dbname(), $exObj->release() );
my $dbRef;
if( ($dbRef) = $sth->fetchrow_array() ) {
$dbJustInserted = 0;
} else {
# store it, get dbID for that
$sth = $self->prepare( "
INSERT ignore INTO external_db
SET db_name = ?,
release = ?,
status = ?
" );
$sth->execute( $exObj->dbname(), $exObj->release(), $exObj->status);
$dbJustInserted = 1;
$sth = $self->prepare( "SELECT LAST_INSERT_ID()" );
$sth->execute();
( $dbRef ) = $sth->fetchrow_array();
if( ! defined $dbRef ) {
$self->throw( "Database entry failed." );
}
}
AND release = ?");
$sth->execute( $exObj->dbname(), $exObj->release() );
my $dbX;
my ($dbRef) = $sth->fetchrow_array();
if(!$dbRef) {
$self->throw("external_db [" . $exObj->db_name . "] release [" .
$exObj->release . "] does not exist");
}
if( $dbJustInserted ) {
# dont have to check for existence; cannnot have been inserted at
# this point, so $dbX is certainly undefined
$dbX = undef;
} else {
$sth = $self->prepare( "
#
# Check for the existance of the external reference, add it if not present
#
$sth = $self->prepare( "
SELECT xref_id
FROM xref
WHERE external_db_id = ?
AND dbprimary_acc = ?
AND version = ?
" );
$sth->execute( $dbRef, $exObj->primary_id(),
$exObj->version() );
( $dbX ) = $sth->fetchrow_array();
}
AND version = ?" );
$sth->execute( $dbRef, $exObj->primary_id(),$exObj->version() );
my ($dbX) = $sth->fetchrow_array();
$sth->finish();
if( ! defined $dbX ) {
$sth = $self->prepare( "
INSERT ignore INTO xref
if(!$dbX) {
#
# store the new xref
#
$sth = $self->prepare( "
INSERT ignore INTO xref
SET dbprimary_acc = ?,
display_label = ?,
version = ?,
description = ?,
external_db_id = ?
" );
$sth->execute( $exObj->primary_id(), $exObj->display_id(), $exObj->version(),
$exObj->description(), $dbRef);
$sth = $self->prepare( "
SELECT LAST_INSERT_ID()
" );
$sth->execute();
( $dbX ) = $sth->fetchrow_array();
external_db_id = ?" );
$sth->execute( $exObj->primary_id(), $exObj->display_id(),
$exObj->version(), $exObj->description(), $dbRef);
$dbX = $sth->{'mysql_insertid'};
$sth->finish();
# synonyms
my $synonyms = $exObj->get_all_synonyms();
foreach my $syn ( @{$synonyms} ) {
#Check if this synonym is already in the database for the given primary id
my $sth = $self->prepare( "
SELECT xref_id,
synonym
FROM external_synonym
WHERE xref_id = ?
AND synonym = ?
" );
$sth->execute($dbX, $syn);
my ($dbSyn) = $sth->fetchrow_array();
#print STDERR $dbSyn[0],"\n";
if( ! $dbSyn ) {
$sth = $self->prepare( "
INSERT ignore INTO external_synonym
SET xref_id = ?,
synonym = ?
" );
$sth->execute($dbX, $syn);
}
}
$sth = $self->prepare( "
INSERT ignore INTO object_xref
SET xref_id = ?,
ensembl_object_type = ?,
ensembl_id = ?
" );
$sth->execute( $dbX, $ensType, $ensObject );
$exObj->dbID( $dbX );
$exObj->adaptor( $self );
if ($exObj->isa('Bio::EnsEMBL::IdentityXref')) {
$sth = $self->prepare( "
SELECT LAST_INSERT_ID()
" );
$sth->execute();
my ( $Xidt ) = $sth->fetchrow_array();
$sth = $self->prepare( "
INSERT ignore INTO identity_xref
SET object_xref_id = ?,
query_identity = ?,
target_identity = ?
" );
$sth->execute( $Xidt, $exObj->query_identity, $exObj->target_identity );
}
} else {
$sth = $self->prepare ( "
SELECT xref_id
FROM object_xref
WHERE xref_id = ?
AND ensembl_object_type = ?
AND ensembl_id = ?
");
#
# store the synonyms for the new xref
#
my $synonym_check_sth = $self->prepare(
"SELECT xref_id, synonym
FROM external_synonym
WHERE xref_id = ?
AND synonym = ?");
my $synonym_store_sth = $self->prepare(
"INSERT ignore INTO external_synonym
SET xref_id = ?, synonym = ?");
my $synonyms = $exObj->get_all_synonyms();
foreach my $syn ( @$synonyms ) {
$synonym_check_sth->execute($dbX, $syn);
my ($dbSyn) = $sth->fetchrow_array();
$synonym_store_sth->execute($dbX, $syn) if(!$dbSyn);
}
$sth->execute($dbX, $ensType, $ensObject);
my ($tst) = $sth->fetchrow_array;
if (! defined $tst) {
# line is already in xref table. Need to add to object_xref
$sth = $self->prepare( "
INSERT ignore INTO object_xref
SET xref_id = ?,
ensembl_object_type = ?,
ensembl_id = ?
");
$synonym_check_sth->finish();
$synonym_store_sth->finish();
}
#
# check if the object mapping was already stored
#
$sth = $self->prepare (
"SELECT xref_id
FROM object_xref
WHERE xref_id = ?
AND ensembl_object_type = ?
AND ensembl_id = ?");
$sth->execute($dbX, $ensType, $ensObject);
my ($tst) = $sth->fetchrow_array;
$sth->finish();
if(!$tst) {
#
# Store the reference to the internal ensembl object
#
$sth = $self->prepare(
"INSERT ignore INTO object_xref
SET xref_id = ?, ensembl_object_type = ?, ensembl_id = ?");
$sth->execute( $dbX, $ensType, $ensObject );
$exObj->dbID( $dbX );
$exObj->adaptor( $self );
if ($exObj->isa('Bio::EnsEMBL::IdentityXref')) {
$sth = $self->prepare( "
SELECT LAST_INSERT_ID()
" );
$sth->execute();
my ( $Xidt ) = $sth->fetchrow_array();
$sth = $self->prepare( "
$sth->execute( $dbX, $ensType, $ensObject );
$exObj->dbID( $dbX );
$exObj->adaptor( $self );
my $Xidt = $sth->{'mysql_insertid'};
#
# If this is an IdentityXref need to store in that table too
#
if ($exObj->isa('Bio::EnsEMBL::IdentityXref')) {
$sth = $self->prepare( "
INSERT ignore INTO identity_xref
SET object_xref_id = ?,
query_identity = ?,
target_identity = ?
" );
$sth->execute( $Xidt, $exObj->query_identity, $exObj->target_identity );
}
}
target_identity = ?" );
$sth->execute($Xidt, $exObj->query_identity, $exObj->target_identity);
}
return $dbX;
}
return $dbX;
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment