From 69bacbf38c9dedfab9612e7fe85174e488a77a57 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Thu, 17 Apr 2003 09:34:46 +0000
Subject: [PATCH] DBEntryAdaptor::store changed so can no longer add
external_db entries and refactored a bit
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 253 ++++++++------------
1 file changed, 95 insertions(+), 158 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 3392340eb1..5228ba073c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -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;
}
--
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