From f32dd2657f5bff969bcc33fc30f9f1113a3fb155 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 1 Nov 2012 16:12:48 +0000
Subject: [PATCH] [ENSCORESW-301]. Adding INSERT IGNORE to a lot of statements
as EFO can repeat terms and subsets from other ontologies.
---
.../ontology/scripts/load_OBO_file.pl | 75 ++++++++++---------
1 file changed, 40 insertions(+), 35 deletions(-)
diff --git a/misc-scripts/ontology/scripts/load_OBO_file.pl b/misc-scripts/ontology/scripts/load_OBO_file.pl
index 840fb91c10..4bef63d44b 100755
--- a/misc-scripts/ontology/scripts/load_OBO_file.pl
+++ b/misc-scripts/ontology/scripts/load_OBO_file.pl
@@ -110,11 +110,12 @@ sub write_subset {
$dbh->do("LOCK TABLE subset WRITE");
- my $statement = "INSERT INTO subset " . "(name, definition) " . "VALUES (?,?)";
+ my $statement = q{INSERT IGNORE INTO subset (name, definition) VALUES (?,?)};
+ my $lookup_sql = 'select subset_id from subset where name =?';
my $sth = $dbh->prepare($statement);
+ my $lookup_sth = $dbh->prepare($lookup_sql);
- my $id;
my $count = 0;
local $SIG{ALRM} = sub {
@@ -135,18 +136,23 @@ sub write_subset {
$sth->bind_param(2, $subset->{'definition'}, SQL_VARCHAR);
$sth->execute();
-
- if (!defined($id)) {
- $id = $dbh->last_insert_id(undef, undef, 'subset', 'subset_id');
- }
- else {
- ++$id;
- }
+
+ my $id = $dbh->last_insert_id(undef, undef, 'subset', 'subset_id');
+ if(! $id) {
+ $lookup_sth->bind_param(1, $subset->{name}, SQL_VARCHAR);
+ $lookup_sth->execute();
+ ($id) = $lookup_sth->fetchrow_array();
+ printf(STDERR "CLASH: SUBSET '%s' already exists in this database. Reusing ID %d\n", $subset->{name}, $id);
+ }
+
$subset->{'id'} = $id;
++$count;
}
alarm(0);
+
+ $lookup_sth->finish();
+ $sth->finish();
$dbh->do("OPTIMIZE TABLE term");
$dbh->do("UNLOCK TABLES");
@@ -163,7 +169,7 @@ sub write_term {
$dbh->do("LOCK TABLES term WRITE, synonym WRITE");
- my $statement = "INSERT INTO term " . "(ontology_id, subsets, accession, name, definition) " . "VALUES (?,?,?,?,?)";
+ my $statement = "INSERT IGNORE INTO term (ontology_id, subsets, accession, name, definition) VALUES (?,?,?,?,?)";
my $syn_stmt = "INSERT INTO synonym (term_id, name) VALUES (?,?)";
@@ -176,7 +182,6 @@ sub write_term {
my $syn_sth = $dbh->prepare($syn_stmt);
my $existing_term_sth = $dbh->prepare($existing_term_st);
- my $id;
my $count = 0;
my $updated_count = 0;
my $syn_count = 0;
@@ -191,6 +196,7 @@ sub write_term {
my $term = $terms->{$accession};
my $term_subsets;
+ my $reuse = 0;
if (exists($term->{'subsets'})) {
$term_subsets = join(',', map { $subsets->{$_}{'name'} } @{$term->{'subsets'}});
@@ -205,23 +211,14 @@ sub write_term {
$term->{'id'} = $existing_term_id;
}
else {
-
#if not link it to Unknown ontology
-
$sth->bind_param(1, $unknown_onto_id, SQL_INTEGER);
$sth->bind_param(2, $term_subsets, SQL_VARCHAR);
$sth->bind_param(3, $term->{'accession'}, SQL_VARCHAR);
$sth->bind_param(4, 'UNKNOWN NAME', SQL_VARCHAR);
$sth->bind_param(5, 'UNKNOWN DEFINITION', SQL_VARCHAR);
-
$sth->execute();
-
- if (!defined($id)) {
- $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
- }
- else {
- ++$id;
- }
+ my $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
$term->{'id'} = $id;
++$count;
}
@@ -255,25 +252,33 @@ sub write_term {
$sth->bind_param(5, $term->{'definition'}, SQL_VARCHAR);
$sth->execute();
-
- if (!defined($id)) {
- $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
- }
- else {
- ++$id;
+ my $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
+ if(! $id) {
+ $existing_term_sth->execute($term->{'accession'});
+ my ($existing_term_id, $ontology_id) = $existing_term_sth->fetchrow_array;
+ $id = $existing_term_id;
+ printf(STDERR "CLASH: TERM '%s' already exists in this database. Reusing ID %d\n", $term->{accession}, $existing_term_id);
+ $reuse = 1;
}
$term->{'id'} = $id;
++$count;
}
-
- foreach my $syn (@{$term->{'synonyms'}}) {
- $syn_sth->bind_param(1, $id, SQL_INTEGER);
- $syn_sth->bind_param(2, $syn, SQL_VARCHAR);
-
- $syn_sth->execute();
-
- ++$syn_count;
+
+ if(@{$term->{synonyms}}) {
+ if($reuse) {
+ print STDERR "REUSE: Skipping synonym writing as term already exists in this database\n";
+ }
+ else {
+ foreach my $syn (@{$term->{'synonyms'}}) {
+ $syn_sth->bind_param(1, $term->{id}, SQL_INTEGER);
+ $syn_sth->bind_param(2, $syn, SQL_VARCHAR);
+
+ $syn_sth->execute();
+
+ ++$syn_count;
+ }
+ }
}
}
} ## end foreach my $accession ( sort...)
--
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