From 4573a115f2bc4276d01a44ff9c7db2d2fd4b093b Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 1 Apr 2005 13:30:26 +0000
Subject: [PATCH] Added support for parsing from databases (rather than files).
---
.../xref_mapping/XrefParser/BaseParser.pm | 26 ++++++++++++++-----
1 file changed, 20 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index fab97c9d96..f9f9add7d1 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -85,9 +85,10 @@ sub run {
# Download each source into the appropriate directory for parsing later
+ # or call the appropriate database parser if appropriate
# Also delete previous working directory if we're starting a new source type
- #can have more than one file
+ # can have more than one file
my @files = split(/\s+/,$url);
@@ -97,14 +98,27 @@ sub run {
my $type = $name;
my @new_file=();
$dir = $base_dir . "/" . sanitise($type);
+ my $dsn;
foreach my $urls (@files){
+
+ # Database parsing
+ if ($urls =~ /^mysql:/i) {
+ $dsn = $urls;
+ print "Parsing $dsn with $parser\n";
+ eval "require XrefParser::$parser";
+ my $new = "XrefParser::$parser"->new();
+ $new->run($dsn, $source_id, $species_id);
+ next;
+ }
+
my ($file) = $urls =~ /.*\/(.*)/;
+ # File parsing
if (!$skipdownload) {
-
+
rmtree $dir if ($type ne $last_type);
mkdir $dir if (!-e $dir);
-
+
$last_type = $type;
print "Downloading $urls to $dir/$file\n";
@@ -123,7 +137,7 @@ sub run {
system("gunzip -f $dir/$file");
$file = $1;
}
-
+
}
else{
if ($file =~ /(.*)\.gz$/) {
@@ -164,8 +178,8 @@ sub run {
# set release if specified
set_release($release, $source_id) if ($release);
- }
- elsif(!$empty){
+ }
+ elsif(!$dsn && !$empty){
print "Ignoring ".join(' ',@new_file)." as checksums match\n";
}
--
GitLab