From 6c3413e2e85c4cbf7f8b7e7222c40a551a780e93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 19 Oct 2011 10:41:34 +0000
Subject: [PATCH] Make this upload stable IDs into release 65 databases
correctly.
---
modules/Bio/EnsEMBL/IdMapping/BaseObject.pm | 108 +++++++++++++++-----
1 file changed, 80 insertions(+), 28 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm b/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
index 3177940292..22f9621af6 100644
--- a/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
@@ -302,63 +302,115 @@ sub dump_table_to_file {
=cut
sub upload_file_into_table {
- my $self = shift;
- my $dbtype = shift;
- my $table = shift;
- my $filename = shift;
+ my $self = shift;
+ my $dbtype = shift;
+ my $table = shift;
+ my $filename = shift;
my $no_check_empty = shift;
# argument check
- unless (($dbtype eq 'source') or ($dbtype eq 'target')) {
+ unless ( ( $dbtype eq 'source' ) or ( $dbtype eq 'target' ) ) {
throw("Missing or unknown db type: $dbtype.");
}
throw("Need a table name.") unless ($table);
- throw("Need a filename.") unless ($filename);
+ throw("Need a filename.") unless ($filename);
# sanity check for dry run
- if ($self->conf->param('dry_run')) {
- $self->logger->warning("dry_run - skipping db upload for $filename.\n");
+ if ( $self->conf->param('dry_run') ) {
+ $self->logger->warning(
+ "dry_run - skipping db upload for $filename.\n");
return;
}
-
- my $file = join('/', $self->conf->param('basedir'), 'tables', $filename);
+
+ my $file =
+ join( '/', $self->conf->param('basedir'), 'tables', $filename );
my $r = 0;
-
- if (-s $file) {
- $self->logger->debug("$file -> $table\n", 1);
-
+ if ( -s $file ) {
+
+ $self->logger->debug( "$file -> $table\n", 1 );
+
my $dba = $self->cache->get_DBAdaptor($dbtype);
my $dbh = $dba->dbc->db_handle;
+ my $idtable = 0;
+ if ( $table =~ /^([^_]+)_stable_id/ ) {
+ # This is a stable_id table we're working with.
+ $idtable = 1;
+ $table = $1;
+ }
+
# check table is empty
- my ($sql, $sth);
+ my ( $sql, $sth );
unless ($no_check_empty) {
- $sql = qq(SELECT count(*) FROM $table);
+ if ($idtable) {
+ $sql =
+ qq(SELECT count(*) FROM $table WHERE stable_id IS NOT NULL);
+ }
+ else {
+ $sql = qq(SELECT count(*) FROM $table);
+ }
$sth = $dbh->prepare($sql);
$sth->execute;
my ($c) = $sth->fetchrow_array;
$sth->finish;
- if ($c) {
- $self->logger->warning("Table $table not empty: found $c entries.\n", 1);
- $self->logger->info("Data not uploaded!\n", 1);
+ if ( $c > 0 ) {
+ if ($idtable) {
+ $self->logger->warning(
+ "Table $table contains $c stable IDs.\n",
+ 1 );
+ }
+ else {
+ $self->logger->warning(
+ "Table $table not empty: found $c entries.\n",
+ 1 );
+ }
+ $self->logger->info( "Data not uploaded!\n", 1 );
return $r;
}
- }
-
+ } ## end unless ($no_check_empty)
+
# now upload the data
- $sql = qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE $table);
- $sth = $dbh->prepare($sql);
- $r = $sth->execute;
- $sth->finish;
+ if ($idtable) {
+ # Create a temporary table, upload the data into it, and then
+ # update the main table.
+ $dbh->do(
+ qq( CREATE TABLE stable_id_$$ ( object_id INTEGER UNSIGNED,
+ stable_id VARCHAR(255),
+ version SMALLINT UNSIGNED,
+ created_date DATETIME,
+ modified_date DATETIME,
+ PRIMARY KEY(object_id) ) )
+ );
+
+ $dbh->do(
+ qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE stable_id_$$));
+
+ $dbh->do(
+ qq(
+ UPDATE TABLE $table, stable_id_$$
+ SET $table.stable_id=stable_id_$$.stable_id,
+ $table.version=stable_id_$$.version,
+ $table.created_date=stable_id_$$.created_date,
+ $table.modified_date=stable_id_$$.modified_date
+ WHERE $table.${table}_id = stable_id_$$.object_id )
+ );
+
+ $dbh->do(qq(DROP TABLE stable_id_$$));
+ } ## end if ($idtable)
+ else {
+ $dbh->do(qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE $table));
+ }
+ $dbh->do(qq(OPTIMIZE TABLE $table));
- } else {
- $self->logger->warning("No data found in file $filename.\n", 1);
+ } ## end if ( -s $file )
+ else {
+ $self->logger->warning( "No data found in file $filename.\n", 1 );
}
return $r;
-}
+} ## end sub upload_file_into_table
=head2 logger
--
GitLab