From 7c06bc20fb44fdc15cf6c7eb7db1836b9567e017 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 23 Oct 2006 07:20:45 +0000
Subject: [PATCH] Better handling of multi-species dumps.
---
misc-scripts/ebi_search_dump/dump_ebi.pl | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/ebi_search_dump/dump_ebi.pl b/misc-scripts/ebi_search_dump/dump_ebi.pl
index 9db8fc8904..63e6dbdcbe 100644
--- a/misc-scripts/ebi_search_dump/dump_ebi.pl
+++ b/misc-scripts/ebi_search_dump/dump_ebi.pl
@@ -1,6 +1,8 @@
# Dump gene and xref information to an XML file for indexing by the EBI's
# search engine.
-
+#
+# To copy files to the EBI so that they can be picked up:
+# scp homo_sapiens_core_41_36c.xml.gz glenn@puffin.ebi.ac.uk:xml/
use strict;
use DBI;
@@ -28,7 +30,7 @@ if( !$host || !$dbpattern ) {
usage();
}
-my $entry_count = 0;
+my $entry_count ;
my $fh;
@@ -37,7 +39,6 @@ run();
sub run() {
# loop over databases
- # TODO - separate file for each database?
my $dsn = "DBI:mysql:host=$host";
$dsn .= ";port=$port" if ($port);
@@ -70,7 +71,8 @@ sub run() {
'-port' => $port,
'-user' => $user,
'-pass' => $pass,
- '-dbname' => $dbname);
+ '-dbname' => $dbname,
+ '-species' => $dbname);
header($dba, $dbname);
@@ -114,6 +116,8 @@ sub content {
my ($dba) = @_;
+ $entry_count = 0;
+
my $gene_adaptor = $dba->get_GeneAdaptor();
foreach my $gene (@{$gene_adaptor->fetch_all()}) {
--
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