[Cogs-guts] ensupdate getensembl.pl,1.7,1.8

[kirovs <ki...@us...>]

Update of /cvsroot/cogs/ensupdate
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv14538

Modified Files:
	getensembl.pl 
Log Message:
added mysql connect params, wget alt, bugs

Index: getensembl.pl
===================================================================
RCS file: /cvsroot/cogs/ensupdate/getensembl.pl,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** getensembl.pl	6 Dec 2005 14:58:55 -0000	1.7
--- getensembl.pl	14 Sep 2007 18:06:12 -0000	1.8
***************
*** 7,11 ****
  #   changes to remote directory <rmtdir>
  #   puts files in the local directory <locdir>
! 
  
  # Load the Net::FTP package
--- 7,12 ----
  #   changes to remote directory <rmtdir>
  #   puts files in the local directory <locdir>
! use lib '/perl/newlib/ia64-linux-multi-stdio';
! #use lib '/perl/newlib/ia64-linux-multi-stdio/auto';
  
  # Load the Net::FTP package
***************
*** 18,24 ****
  my $host=$ENV{ENS_HOST};
  my $sock=$ENV{ENS_SOCK};
  $enslogin=$user;
  my $sid='ensembl_databases';
! my $cs = "dbi:mysql:$sid:$host;mysql_socket=$sock";
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
  my $currenth=$dbh->prepare("select db_name, version from ens_dbnames where current = 'yes'")||die "Couldn't prepare the select statement\n";
--- 19,26 ----
  my $host=$ENV{ENS_HOST};
  my $sock=$ENV{ENS_SOCK};
+ my $port=$ENV{ENS_PORT};
  $enslogin=$user;
  my $sid='ensembl_databases';
! my $cs = "dbi:mysql:$sid:$host;mysql_socket=$sock;port=$port";
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
  my $currenth=$dbh->prepare("select db_name, version from ens_dbnames where current = 'yes'")||die "Couldn't prepare the select statement\n";
***************
*** 77,81 ****
    my @cl=split(/\s/,$db);
    my $name=pop @cl;
!   $ftp->cwd("$name/data/mysql")||die;
    my @all=$ftp->dir;
   foreach my $d (@all) {
--- 79,83 ----
    my @cl=split(/\s/,$db);
    my $name=pop @cl;
!   $ftp->cwd("$name/data/mysql")||die $name;
    my @all=$ftp->dir;
   foreach my $d (@all) {
***************
*** 100,104 ****
   next unless ($current{$core}<$v1);
  next if (-e $core);
!  $ftp->cwd("$core")||die;
   print "Working on $core\n";
   push @cores,$core;#Remember the DB names
--- 102,106 ----
   next unless ($current{$core}<$v1);
  next if (-e $core);
!  $ftp->cwd("$core")||die $@,$core;
   print "Working on $core\n";
   push @cores,$core;#Remember the DB names
***************
*** 106,109 ****
--- 108,112 ----
   chdir($core);
   my @files=grep (!/total/,$ftp->dir);
+ my $cf=$ftp->pwd;
   foreach my $file (@files) {
    my @long=split(/\s+/,$file);
***************
*** 114,118 ****
  	next if (-e $dfile);
     print "Getting $gfile..\n";
!    $ftp->get($gfile);
  #Gunzip as we go
     system ("gunzip $gfile &");
--- 117,124 ----
  	next if (-e $dfile);
     print "Getting $gfile..\n";
!    #$ftp->get($gfile);
! my $cloc="ftp:\/\/ftp.ensembl.org/$cf/$gfile";
! print $cloc,"\n";
!   unless  (system("wget $cloc")==0) { warn "No $cloc"; next; }
  #Gunzip as we go
     system ("gunzip $gfile &");
***************
*** 120,126 ****
   print "Done with $core\n";
   chdir("..");
!  $ftp->cwd('..');
  }
   $ftp->cwd("../../..");
  
  }
--- 126,141 ----
   print "Done with $core\n";
   chdir("..");
!  unless ($ftp->pwd) {
!   $ftp = Net::FTP->new($host) or
!       die "Cannot contact $host\n:$!";
!  $ftp->login('anonymous', $enslogin) or
!        die "Cannot login ($host)\n:". $ftp->message;
! }
!  $ftp->cwd("/$cf")||die "CF: $cf";
!  $ftp->cwd("..");
!  print 'CW1',$ftp->pwd,"\n";
  }
   $ftp->cwd("../../..");
+  print 'CW2',$ftp->pwd,"\n";
  
  }