From 55f7ace4a1b60f3476ce6dc64f786e50a78490cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 21 Feb 2007 17:29:14 +0000
Subject: [PATCH] Set skipdownload=0 if checkdownload==1 and if the file does
not exist. Otherwise, if a previous file exists (with checkdownload==1),
skipdownload would be 1 and the missing files would not be downloaded...
Fixes spurious FAILs because of missing data.
---
.../xref_mapping/XrefParser/BaseParser.pm | 39 ++++++++++++-------
1 file changed, 24 insertions(+), 15 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 7cbb79fd6a..9b368624af 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -193,21 +193,28 @@ sub run {
print "Using $file_from_archive from $file\n";
}
- if ( $checkdownload ) {
-
- my $check_file = "$dir/$file" ;
- $check_file =~s/\.gz//;
- $check_file =~s/\.Z//;
- print "checking for file $check_file\n" ;
- if (-e "$check_file" ) {
- print "SKIPPING $file because file $check_file already exists\n" ;
- $skipdownload = 1 ;
- $file =~s/\.gz//;
- $file=~s/\.Z//;
- } else {
- print "File $check_file does not exist. \n scheduling $dir/$file for download ..........\n" ;
+ if ($checkdownload) {
+ my $check_file = $dir . '/' . $file;
+ $check_file =~ s/\.gz$//;
+ $check_file =~ s/\.Z$//;
+
+ print "Checking for file '$check_file'\n";
+
+ if ( -e "$check_file" ) {
+ print "SKIPPING $file because file "
+ . "'$check_file' already exists\n";
+
+ $skipdownload = 1;
+
+ $file =~ s/\.gz$//;
+ $file =~ s/\.Z$//;
+ } else {
+ print "File '$check_file' does not exist.\n"
+ . "Scheduling '$dir/$file' for download...\n";
+
+ $skipdownload = 0;
}
- }
+ }
$file =~ s/[&=]//g;
@@ -239,7 +246,9 @@ sub run {
my $num_attempts = 0;
my $missing = 1;
while($num_attempts < 5 and $missing){
- my $result = system("wget", "--quiet","--directory-prefix=$dir", "--output-document=$dir/$file", $urls );
+ my $result =
+ system( "wget", "--quiet", "--directory-prefix=$dir",
+ "--output-document=$dir/$file", $urls );
# check that the file actually downloaded; may not (e.g. if too many anonymous users)
if ($result != 0) {
--
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