From 5b63dd6386a803c264f400278d7ba4d39b0a1b11 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 26 Jul 2004 08:54:33 +0000
Subject: [PATCH] Check if an xref exists when inserting, if not use the new
ID, if it does exist, use the existing xref_id.
---
misc-scripts/xref_mapping/BaseParser.pm | 55 ++++++++++++++++++++++---
1 file changed, 50 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/xref_mapping/BaseParser.pm b/misc-scripts/xref_mapping/BaseParser.pm
index 41b9ea2697..d72e266686 100644
--- a/misc-scripts/xref_mapping/BaseParser.pm
+++ b/misc-scripts/xref_mapping/BaseParser.pm
@@ -157,6 +157,9 @@ sub upload_xrefs {
my $syn_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?,?)");
my $dep_sth = $dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)");
+ local $xref_sth->{RaiseError}; # disable error handling here as we'll do it ourselves
+ local $xref_sth->{PrintError};
+
foreach my $xref (@xrefs) {
# Create entry in xref table and note ID
@@ -164,10 +167,11 @@ sub upload_xrefs {
$xref->{LABEL},
$xref->{DESCRIPTION},
$xref->{SOURCE_ID},
- $xref->{SPECIES_ID}) || die $dbi->errstr;
+ $xref->{SPECIES_ID});
- # get ID of xref just inserted
- my $xref_id = $xref_sth->{'mysql_insertid'};
+ # If there was an error, an xref with the same acc & source already exists.
+ # If so, find its ID, otherwise get ID of xref just inserted
+ my $xref_id = insert_or_select($xref_sth, $dbi->err, $xref->{ACCESSION}, $xref->{SOURCE_ID});
# create entry in primary_xref table with sequence
# TODO experimental/predicted????
@@ -184,9 +188,10 @@ sub upload_xrefs {
$xref->{LABEL},
$xref->{DESCRIPTION},
$xref->{SOURCE_ID},
- $xref->{SPECIES_ID}) || die $dbi->errstr;
+ $xref->{SPECIES_ID});
+
+ my $syn_xref_id = insert_or_select($xref_sth, $dbi->err, $syn, $xref->{SOURCE_ID});
- my $syn_xref_id = $xref_sth->{'mysql_insertid'};
$syn_sth->execute($xref_id, $syn_xref_id, $xref->{SOURCE_ID} ) || die $dbi->errstr;
} # foreach syn
@@ -339,6 +344,46 @@ sub md5sum {
}
+# --------------------------------------------------------------------------------
+
+sub get_xref_id_by_accession_and_source {
+
+ my ($acc, $source_id) = @_;
+
+ my $dbi = dbi();
+ my $sth = $dbi->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=?");
+ $sth->execute($acc, $source_id) || die $dbi->errstr;
+ my @row = $sth->fetchrow_array();
+ my $xref_id = $row[0];
+
+ return $xref_id;
+
+}
+
+# --------------------------------------------------------------------------------
+# If there was an error, an xref with the same acc & source already exists.
+# If so, find its ID, otherwise get ID of xref just inserted
+
+sub insert_or_select {
+
+ my ($sth, $error, $acc, $source) = @_;
+
+ my $id;
+
+ if ($error) {
+
+ $id = get_xref_id_by_accession_and_source($acc, $source);
+ print "Got existing xref id " . $id . " for " . $acc . " " . $source . "\n";
+
+ } else {
+
+ $id = $sth->{'mysql_insertid'};
+
+ }
+
+ return $id;
+
+}
# --------------------------------------------------------------------------------
--
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