From c16ff7c2add9d3d706962e86f34c61485ef07129 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 4 Aug 2011 16:00:41 +0000
Subject: [PATCH] In parsing_finished_store_data():
If the table (either xref or object_xref) is empty, $max_val will be
undefined. Make sure that we substitute 1 for it in this case when
calling add_meta_pair().
---
.../xref_mapping/XrefParser/BaseParser.pm | 34 +++++++++----------
1 file changed, 17 insertions(+), 17 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 0bd884d7bd..f23f72af8b 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -2414,36 +2414,36 @@ sub get_ext_synonyms{
# Store data needed to beable to revert to same stage as after parsing
#
-sub parsing_finished_store_data{
+sub parsing_finished_store_data {
my $self = shift;
-# Store max id for
+ # Store max id for
-# gene/transcript/translation_direct_xref general_xref_id #Does this change??
+ # gene/transcript/translation_direct_xref general_xref_id #Does this change??
-# xref xref_id
+ # xref xref_id
+ # dependent_xref object_xref_id is all null
+ # go_xref object_xref_id
+ # object_xref object_xref_id
+ # identity_xref object_xref_id
-# dependent_xref object_xref_id is all null
-
-# go_xref object_xref_id
-# object_xref object_xref_id
-# identity_xref object_xref_id
-
- my %table_and_key = ('xref' => "xref_id", 'object_xref' => "object_xref_id");
+ my %table_and_key =
+ ( 'xref' => "xref_id", 'object_xref' => "object_xref_id" );
my $dbi = $self->dbi();
- foreach my $table (keys %table_and_key){
-# print "select MAX(".$table_and_key{$table}.") from $table\n";
- my $sth = $dbi->prepare("select MAX(".$table_and_key{$table}.") from $table");
+ foreach my $table ( keys %table_and_key ) {
+ my $sth = $dbi->prepare(
+ "select MAX(" . $table_and_key{$table} . ") from $table" );
$sth->execute;
my $max_val;
- $sth->bind_columns(\$max_val);
+ $sth->bind_columns( \$max_val );
$sth->fetch;
- $self->add_meta_pair("PARSED_".$table_and_key{$table}, $max_val);
$sth->finish;
+ $self->add_meta_pair( "PARSED_" . $table_and_key{$table},
+ $max_val || 1 );
}
return;
-}
+} ## end sub parsing_finished_store_data
--
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