From 47b455cfa6184b6d0ef91236482cbb6560e58ef6 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Sun, 17 Apr 2005 13:53:16 +0000
Subject: [PATCH] set flags to disconnect and reconnect either side of the
mapping
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 7296b1bd32..322bdd1e46 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -643,9 +643,16 @@ sub run_mapping {
# delete old output files in target directory if we're going to produce new ones
if (!defined($self->use_existing_mappings())) {
+ print "deleting out err and map files from output dir\n";
my $dir = $self->core->dir();
unlink (<$dir/*.map $dir/*.out $dir/*.err>);
}
+ #disconnect so that we can then reconnect after the long mapping bit.
+ $self->core->dbc->disconnect_if_idle(1);
+ $self->xref->dbc->disconnect_if_idle(1);
+ $self->core->dbc->disconnect_when_inactive(1);
+ $self->xref->dbc->disconnect_when_inactive(1);
+
# foreach method, submit the appropriate job & keep track of the job name
# note we check if use_existing_mappings is set here, not earlier, as we
@@ -792,7 +799,12 @@ sub parse_mappings {
my $dir = $ensembl->dir();
# incase timed out, force reconnection
+ $ensembl->dbc->disconnect_if_idle(0);
+ $ensembl->dbc->disconnect_when_inactive(0);
$ensembl->dbc->connect();
+
+ $xref->dbc->disconnect_if_idle(0);
+ $xref->dbc->disconnect_when_inactive(0);
$xref->dbc->connect();
# get current max object_xref_id
@@ -1193,6 +1205,7 @@ sub get_analysis_id {
print "Done (analysis ID=" . $analysis_id. ")\n";
}
+ $sth->finish();
return $analysis_id;
--
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