From a04811425d84d19adabcb3df1c34eb4aca3610f2 Mon Sep 17 00:00:00 2001
From: Vasily Tokarev <34555288+tokarevvasily@users.noreply.github.com>
Date: Tue, 26 Jan 2021 17:34:10 -0500
Subject: [PATCH] Refresh FTP connection for downloading libraries with
 `--use-ftp`

I had issues with downloading genomes for *viral* library. I have noticed that it could download only first 92 genomes from *manifest.txt*. I am fairly certain that it is something NCBI implemented intentionally (or maybe not).

I have made changes to *rsync_from_ncbi.pl* to refresh FTP connection if genome is not downloaded on the first attempt, otherwise it gives a warning.
---
 scripts/rsync_from_ncbi.pl | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/scripts/rsync_from_ncbi.pl b/scripts/rsync_from_ncbi.pl
index 6ca239c..e4bb56d 100755
--- a/scripts/rsync_from_ncbi.pl
+++ b/scripts/rsync_from_ncbi.pl
@@ -79,16 +79,21 @@
   close MANIFEST;
 }
 
+sub ftp_connection {
+    my $ftp = Net::FTP->new($SERVER, Passive => 1)
+        or die "$PROG: FTP connection error: $@\n";
+    $ftp->login($FTP_USER, $FTP_PASS)
+        or die "$PROG: FTP login error: " . $ftp->message() . "\n";
+    $ftp->binary()
+        or die "$PROG: FTP binary mode error: " . $ftp->message() . "\n";
+    $ftp->cwd($SERVER_PATH)
+        or die "$PROG: FTP CD error: " . $ftp->message() . "\n";
+    return $ftp;
+    }
+
 if ($use_ftp) {
   print STDERR "Step 1/2: Performing ftp file transfer of requested files\n";
-  my $ftp = Net::FTP->new($SERVER, Passive => 1)
-    or die "$PROG: FTP connection error: $@\n";
-  $ftp->login($FTP_USER, $FTP_PASS)
-    or die "$PROG: FTP login error: " . $ftp->message() . "\n";
-  $ftp->binary()
-    or die "$PROG: FTP binary mode error: " . $ftp->message() . "\n";
-  $ftp->cwd($SERVER_PATH)
-    or die "$PROG: FTP CD error: " . $ftp->message() . "\n";
+  my $ftp = ftp_connection();
   open MANIFEST, "<", "manifest.txt"
     or die "$PROG: can't open manifest: $!\n";
   mkdir "all" or die "$PROG: can't create 'all' directory: $!\n";
@@ -99,7 +104,9 @@
       or do {
         my $msg = $ftp->message();
         if ($msg !~ /: No such file or directory$/) {
-          warn "$PROG: unable to download $_: $msg\n";
+          $ftp = ftp_connection();
+          $ftp->get($_)
+            or warn "$PROG: unable to download $_: $msg\n";
         }
       };
   }