From db5370e2a6cde2301fc0e5d65427525cf20c0dee Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 22 May 2009 13:10:58 +0000
Subject: [PATCH] verbose set to be default
---
misc-scripts/xref_mapping/xref_parser.pl | 33 +++++++++++++++++++++---
1 file changed, 29 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_parser.pl b/misc-scripts/xref_mapping/xref_parser.pl
index 2c80407941..deb2ff848e 100644
--- a/misc-scripts/xref_mapping/xref_parser.pl
+++ b/misc-scripts/xref_mapping/xref_parser.pl
@@ -8,12 +8,16 @@ my ( $host, $port, $dbname,
$sources, $checkdownload, $create,
$release, $cleanup, $drop_existing_db,
$deletedownloaded, $dl_path, $notsource,
- $unzip, $stats, $verbose );
+ $unzip, $stats, $notverbose );
+
+my $options = join(" ",@ARGV);
print "Options: ".join(" ",@ARGV)."\n";
$unzip = 0; # Do not decompress gzipped files by default
+$notverbose = 0;
+
GetOptions(
'dbuser|user=s' => \$user,
'dbpass|pass=s' => \$pass,
@@ -28,7 +32,7 @@ GetOptions(
'setrelease=s' => \$release,
'cleanup' => \$cleanup,
'stats' => \$stats,
- 'verbose' => \$verbose,
+ 'notverbose' => \$notverbose,
'notsource=s' => \$notsource,
'drop_db|dropdb!' =>
\$drop_existing_db, # Drop xref db without user interaction
@@ -48,8 +52,18 @@ if ( !$user || !$host || !$dbname ) {
exit(1);
}
+
+print "host os $host\n";
+
my $base_parser = XrefParser::BaseParser->new();
+
+#
+# If any sources are missing then we need to calculate the display xrefs from the core.
+# As the xref database will not have all the data. Using the core is much slower!!
+#
+
+
$base_parser->run(
$host, ( defined $port ? $port : '3306' ),
$dbname, $user,
@@ -58,7 +72,18 @@ $base_parser->run(
$create, $release,
$cleanup, $drop_existing_db,
$deletedownloaded, $dl_path,
- \@notsource, $unzip, $stats, $verbose );
+ \@notsource, $unzip, $stats, !($notverbose) );
+
+$base_parser->add_meta_pair("options",$options);
+
+if($options =~ /source/ ){
+ $base_parser->add_meta_pair("fullmode","no");
+}
+else{
+ $base_parser->add_meta_pair("fullmode","yes");
+}
+
+$base_parser->parsing_finished_store_data();
# --------------------------------------------------------------------------------
@@ -125,7 +150,7 @@ sub usage {
-unzip Decompress gzipped files (default is to use compressed
files).
- -verbose Output messages about the parsing.
+ -notverbose Do not output messages about the parsing. (NOT recomended)
-stats Generate the stats for the number of types of xrefs added.
--
GitLab