From 6995b414ee9c5ffb283f11687a3d7e2b337f20fd Mon Sep 17 00:00:00 2001
From: Will Spooner <whs@sanger.ac.uk>
Date: Wed, 15 Mar 2006 11:44:58 +0000
Subject: [PATCH] During initial source selection, now selects the species in
addition to the species_id. If the source_url is mysql:* the source and
species are fed to the parser as additional args to the run method. Species
and source specific queries can thus be generated
---
.../xref_mapping/XrefParser/BaseParser.pm | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 5d7d4058a9..aef2033fc2 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -73,17 +73,18 @@ sub run {
}
my $sql =
- "SELECT s.source_id, su.source_url_id, s.name, su.url, su.checksum, su.parser, su.species_id " .
- "FROM source s, source_url su " .
+ "SELECT s.source_id, su.source_url_id, s.name, su.url, su.checksum, su.parser, su.species_id, sp.name " .
+ "FROM source s, source_url su, species sp " .
"WHERE s.download='Y' AND su.source_id=s.source_id " .
- $source_sql . $species_sql .
- "ORDER BY s.ordered";
+ "AND su.species_id=sp.species_id " .
+ $source_sql . $species_sql .
+ "ORDER BY s.ordered";
#print $sql . "\n";
my $sth = $dbi->prepare($sql);
$sth->execute();
- my ($source_id, $source_url_id, $name, $url, $checksum, $parser, $species_id);
- $sth->bind_columns(\$source_id, \$source_url_id, \$name, \$url, \$checksum, \$parser, \$species_id);
+ my ($source_id, $source_url_id, $name, $url, $checksum, $parser, $species_id, $species_name);
+ $sth->bind_columns(\$source_id, \$source_url_id, \$name, \$url, \$checksum, \$parser, \$species_id, \$species_name);
my $last_type = "";
my $dir;
my %summary=();
@@ -118,7 +119,7 @@ sub run {
print "Parsing $dsn with $parser\n";
eval "require XrefParser::$parser";
my $new = "XrefParser::$parser"->new();
- if($new->run($dsn, $source_id, $species_id)){
+ if($new->run($dsn, $source_id, $species_id, $name, $species_name)){
$summary{$parser}++;
}
next;
@@ -679,7 +680,7 @@ sub upload_xref_object_graphs {
$xref->{SPECIES_ID});
my $dep_xref_id = insert_or_select($xref_sth, $dbi->err, $dep{ACCESSION}, $dep{SOURCE_ID});
-
+
if($dbi->err){
print STDERR "dbi\t$dbi->err \n$dep{ACCESSION} \n $dep{SOURCE_ID} \n";
}
--
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