From d4050c3bbeb59cc6c07bd51ca9a3402231735c01 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 23 Feb 2006 15:31:08 +0000
Subject: [PATCH] Added get_existing_mappings (utility method for GOParser.pm
only at the moment)
---
.../xref_mapping/XrefParser/BaseParser.pm | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index d1818edd1e..754d1b3f79 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -371,9 +371,8 @@ sub get_source_id_for_source_name {
if (@row) {
$source_id = $row[0];
} else {
- print STDERR "WARNING: There is no entity $source_name in the source-table of the \n" .
- "WARNING: xref-database. The name of the external db name ($source_name) is hardcoded\n" .
- "WARNING: in the parser\n";
+ print STDERR "WARNING: There is no entity $source_name in the source-table of the xref database.\n" .
+ "WARNING:. The external db name ($source_name) is hardcoded in the parser\n";
warn("WARNING: Couldn't get source ID for source name $source_name\n");
$source_id = -1;
@@ -573,17 +572,15 @@ sub get_existing_mappings {
my %mappings;
- my $from_source = get_source_id_for_source_name($from_source_name);
- my $to_source = get_source_id_for_source_name($to_source_name);
-
-print "from source: $from_source_name id $from_source\t\tto source: $to_source_name id $to_source\n";
+ my $from_source = $self->get_source_id_for_source_name($from_source_name);
+ my $to_source = $self->get_source_id_for_source_name($to_source_name);
my $sql = "SELECT dx.dependent_xref_id, x1.accession as dependent, dx.master_xref_id, x2.accession as master FROM dependent_xref dx, xref x1, xref x2 WHERE x1.xref_id=dx.dependent_xref_id AND x2.xref_id=dx.master_xref_id AND x2.source_id=? AND x1.source_id=? AND x1.species_id=? AND x2.species_id=?";
my $sth = dbi()->prepare($sql);
- $sth->execute($to_source_name, $from_source_name, $species_id, $species_id);
+ $sth->execute($to_source, $from_source, $species_id, $species_id);
while(my @row = $sth->fetchrow_array()){
- $mappings{$row[0]} = $row[1];
+ $mappings{$row[1]} = $row[0];
}
print "Got " . scalar(keys(%mappings)) . " $from_source_name -> $to_source_name mappings\n";
--
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