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Commit 2f0a5a30 authored by Glenn Proctor's avatar Glenn Proctor
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Rationalised database connection; lots of calls to $self->xref()->dbi() and... 

Rationalised database connection; lots of calls to $self->xref()->dbi() and $self->dbi() were causing many database connections to be opened and never closed.

Now only uses one connection per database.
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misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+ 31
− 29
View file @ 2f0a5a30
......@@ -50,6 +50,9 @@ my %source_to_external_db;
my %xrefs_written;
my %object_xrefs_written;
my $core_dbi;
my $xref_dbi;
=head2 dump_seqs
Arg[1]: xref object which holds info needed for the dump of xref
......@@ -69,6 +72,10 @@ sub dump_seqs{
my ($self) = @_;
# initialise DB connections
$core_dbi = $self->dbi();
$xref_dbi = $self->xref()->dbi();
$self->dump_xref();
$self->dump_ensembl();
......@@ -129,8 +136,7 @@ sub get_species_id_from_species_name{
my ($xref,$species) = @_;
my $sql = "select species_id from species where name = '".$species."'";
my $dbi = $xref->dbi();
my $sth = $dbi->prepare($sql);
my $sth = $xref_dbi->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
my $species_id;
......@@ -140,7 +146,7 @@ sub get_species_id_from_species_name{
print STDERR "Couldn't get ID for species ".$species."\n";
print STDERR "It must be one of :-\n";
$sql = "select name from species";
$sth = $dbi->prepare($sql);
$sth = $xref_dbi->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
print STDERR $row[0]."\n";
......@@ -148,7 +154,7 @@ sub get_species_id_from_species_name{
die("Please try again :-)\n");
}
$sth->finish();
$dbi->disconnect();
return $species_id;
}
......@@ -194,8 +200,7 @@ sub get_source_id_from_source_name{
my $source_id;
my $sql = "select source_id from source where name = '".$source."'";
my $dbi = $xref->dbi();
my $sth = $dbi->prepare($sql);
my $sth = $xref_dbi->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
if (defined $row[0] and $row[0] ne '') {
......@@ -205,15 +210,15 @@ sub get_source_id_from_source_name{
print STDERR "Couldn't get ID for source ".$source."\n";
print STDERR "It must be one of :-\n";
$sql = "select name from source";
$sth = $dbi->prepare($sql);
$sth = $xref_dbi->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
print STDERR $row[0]."\n";
}
die("Please try again :-)\n");
}
}
$sth->finish();
$dbi->disconnect();
return $source_id;
}
......@@ -723,7 +728,7 @@ sub parse_mappings {
my $dir = $self->dir();
# get current max object_xref_id
my $row = @{$self->dbi()->selectall_arrayref("SELECT MAX(object_xref_id) FROM object_xref")}[0];
my $row = @{$core_dbi->selectall_arrayref("SELECT MAX(object_xref_id) FROM object_xref")}[0];
my $max_object_xref_id = @{$row}[0];
if (!defined $max_object_xref_id) {
print "Can't get highest existing object_xref_id, using 1\n";
......@@ -865,7 +870,7 @@ sub dump_orphan_xrefs() {
# need a double left-join
my $sql = "SELECT x.xref_id, x.accession, x.version, x.label, x.description, x.source_id, x.species_id FROM xref x LEFT JOIN primary_xref px ON px.xref_id=x.xref_id LEFT JOIN dependent_xref dx ON dx.dependent_xref_id=x.xref_id WHERE px.xref_id IS NULL AND dx.dependent_xref_id IS NULL";
my $sth = $self->xref()->dbi()->prepare($sql);
my $sth = $xref_dbi->prepare($sql);
$sth->execute();
my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id);
......@@ -908,7 +913,7 @@ sub dump_direct_xrefs {
# Will need to look up translation stable ID from transcript stable ID, build hash table
print "Building transcript stable ID -> translation stable ID lookup table\n";
my %transcript_stable_id_to_translation_stable_id;
my $trans_sth = $self->dbi()->prepare("SELECT tss.stable_id as transcript, tls.stable_id AS translation FROM translation tl, translation_stable_id tls, transcript_stable_id tss WHERE tss.transcript_id=tl.transcript_id AND tl.translation_id=tls.translation_id");
my $trans_sth = $core_dbi->prepare("SELECT tss.stable_id as transcript, tls.stable_id AS translation FROM translation tl, translation_stable_id tls, transcript_stable_id tss WHERE tss.transcript_id=tl.transcript_id AND tl.translation_id=tls.translation_id");
$trans_sth->execute();
my ($transcript_stable_id, $translation_stable_id);
$trans_sth->bind_columns(\$transcript_stable_id, \$translation_stable_id);
......@@ -922,7 +927,7 @@ sub dump_direct_xrefs {
# SQL / statement handle for getting all direct xrefs
my $xref_sql = "SELECT dx.general_xref_id, dx.ensembl_stable_id, dx.type, dx.linkage_xref, x.accession, x.version, x.label, x.description, x.source_id, x.species_id FROM direct_xref dx, xref x WHERE dx.general_xref_id=x.xref_id";
my $xref_sth = $self->xref()->dbi()->prepare($xref_sql);
my $xref_sth = $xref_dbi->prepare($xref_sql);
$xref_sth->execute();
......@@ -982,7 +987,7 @@ sub dump_interpro {
open (INTERPRO, ">" . $self->dir() . "/interpro.txt");
my $sth = $self->xref()->dbi()->prepare("SELECT * FROM interpro");
my $sth = $xref_dbi->prepare("SELECT * FROM interpro");
$sth->execute();
my ($interpro, $pfam);
......@@ -998,7 +1003,7 @@ sub dump_interpro {
sub build_stable_id_to_internal_id_hash {
my $self = shift;
my ($self) = @_;
my %stable_id_to_internal_id;
......@@ -1007,7 +1012,7 @@ sub build_stable_id_to_internal_id_hash {
print "Caching stable ID -> internal ID links for ${type}s\n";
my $core_sql = "SELECT ${type}_id, stable_id FROM ${type}_stable_id" ;
my $sth = $self->dbi()->prepare($core_sql);
my $sth = $core_dbi->prepare($core_sql);
$sth->execute();
my ($internal_id, $stable_id);
$sth->bind_columns(\$internal_id, \$stable_id);
......@@ -1069,7 +1074,7 @@ sub get_analysis_id {
my $logic_name = $typeToLogicName{lc($ensembl_type)};
my $sth = $self->dbi()->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
my $sth = $core_dbi->prepare("SELECT analysis_id FROM analysis WHERE logic_name='" . $logic_name ."'");
$sth->execute();
my $analysis_id;
......@@ -1082,7 +1087,7 @@ sub get_analysis_id {
} else {
print "No analysis with logic_name $logic_name found, creating ...\n";
$sth = $self->dbi()->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
$sth = $core_dbi->prepare("INSERT INTO analysis (logic_name, created) VALUES ('" . $logic_name. "', NOW())");
# TODO - other fields in analysis table
$sth->execute();
$analysis_id = $sth->{'mysql_insertid'};
......@@ -1110,9 +1115,6 @@ sub dump_core_xrefs {
open (EXTERNAL_SYNONYM, ">$dir/external_synonym.txt");
open (GO_XREF, ">$dir/go_xref.txt");
my $xref_dbi = $self->xref()->dbi();
my $core_dbi = $self->dbi();
# keep a unique list of source IDs to build the external_db table later
my %source_ids;
......@@ -1301,7 +1303,7 @@ sub build_transcript_display_xrefs {
# note %xref_to_source is global
print "Building xref->source mapping table\n";
my $sql = "SELECT x.xref_id, s.name FROM source s, xref x WHERE x.source_id=s.source_id";
my $sth = $self->xref->dbi()->prepare($sql);
my $sth = $xref_dbi->prepare($sql);
$sth->execute();
my ($xref_id, $source_name);
......@@ -1316,7 +1318,7 @@ sub build_transcript_display_xrefs {
# Cache the list of translation->transcript mappings & vice versa
# Nte variables are global
print "Building translation to transcript mappings\n";
my $sth = $self->dbi()->prepare("SELECT translation_id, transcript_id FROM translation");
my $sth = $core_dbi->prepare("SELECT translation_id, transcript_id FROM translation");
$sth->execute();
my ($translation_id, $transcript_id);
......@@ -1453,7 +1455,7 @@ sub build_gene_display_xrefs_and_descriptions {
print "Getting transcripts for all genes\n";
my $sql = "SELECT gene_id, transcript_id FROM transcript";
my $sth = $self->dbi()->prepare($sql);
my $sth = $core_dbi->prepare($sql);
$sth->execute();
my ($gene_id, $transcript_id);
......@@ -1611,7 +1613,7 @@ sub map_source_to_external_db {
# find appropriate external_db_id for each one
my $sql = "SELECT external_db_id FROM external_db WHERE db_name=?";
my $core_sth = $self->dbi()->prepare($sql);
my $core_sth = $core_dbi->prepare($sql);
$core_sth->execute($source_name);
my @row = $core_sth->fetchrow_array();
......@@ -1649,14 +1651,14 @@ sub do_upload {
if ($deleteexisting) {
$sth = $self->dbi()->prepare("DELETE FROM $table");
$sth = $core_dbi->prepare("DELETE FROM $table");
print "Deleting existing data in $table\n";
$sth->execute();
}
# don't seem to be able to use prepared statements here
$sth = $self->dbi()->prepare("LOAD DATA INFILE \'$file\' INTO TABLE $table");
$sth = $core_dbi->prepare("LOAD DATA INFILE \'$file\' INTO TABLE $table");
print "Uploading data in $file to $table\n";
$sth->execute();
......@@ -1670,7 +1672,7 @@ sub do_upload {
if ($deleteexisting) {
$sth = $self->dbi()->prepare("UPDATE $table SET display_xref_id=NULL");
$sth = $core_dbi->prepare("UPDATE $table SET display_xref_id=NULL");
print "Setting all existing display_xref_id in $table to null\n";
$sth->execute();
......@@ -1681,7 +1683,7 @@ sub do_upload {
#my $str = "mysql -u " .$self->user() ." -p" . $self->password() . " -h " . $self->host() ." -P " . $self->port() . " " .$self->dbname() . " < $file";
#system $str;
$sth = $self->dbi()->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
$sth = $core_dbi->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
open(DX_TXT, $file);
while (<DX_TXT>) {
my ($xref_id, $object_id) = split;
......
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