[Cogs-guts] ensupdate getensembl.pl,1.8,1.9

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

Update of /cvsroot/cogs/ensupdate
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv29078

Modified Files:
	getensembl.pl 
Log Message:
New ftp rep structure, some bugs

Index: getensembl.pl
===================================================================
RCS file: /cvsroot/cogs/ensupdate/getensembl.pl,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** getensembl.pl	14 Sep 2007 18:06:12 -0000	1.8
--- getensembl.pl	23 Oct 2007 20:23:24 -0000	1.9
***************
*** 28,32 ****
  my @current=@{$currenth->fetchall_arrayref};
  foreach my $val (@current) {
!   $current{$val->[0]}=$val->[1];
  }
  my $prefix=$ENV{ENS_DATA};
--- 28,34 ----
  my @current=@{$currenth->fetchall_arrayref};
  foreach my $val (@current) {
! 	my @dat=split(/_/,$val->[0]);
! 	my $cn=join('_',@dat[0..2]);
! 	$current{$cn}=$val->[1];
  }
  my $prefix=$ENV{ENS_DATA};
***************
*** 70,74 ****
  	}
  }
! $ftp->cwd($lr)||die;
  
    print "Retrieving files\n";
--- 72,76 ----
  	}
  }
! $ftp->cwd("$lr/mysql")||die;
  
    print "Retrieving files\n";
***************
*** 77,89 ****
  #This is only for the core DB- get
  foreach my $db (@dbs) {
!   my @cl=split(/\s/,$db);
!   my $name=pop @cl;
!   $ftp->cwd("$name/data/mysql")||die $name;
!   my @all=$ftp->dir;
!  foreach my $d (@all) {
!   if ($#list>-1) {
  	 my $req;           #Check if this DB is requested
  	foreach my $target (@list) {
! 		if ($d=~/$target/) {
  			$req++;
  			last;
--- 79,86 ----
  #This is only for the core DB- get
  foreach my $db (@dbs) {
! 	if ($#list>-1) {
  	 my $req;           #Check if this DB is requested
  	foreach my $target (@list) {
! 		if ($db=~/$target/) {
  			$req++;
  			last;
***************
*** 92,98 ****
    next unless ($req);
    }
! 
!  my @long=split(/\s/,$d);
!  my $core=pop @long;
  #Check if newer
    my @dat=split(/_/,$core);
--- 89,94 ----
    next unless ($req);
    }
!     my @cl=split(/\s/,$db);
!   my $core=pop @cl;
  #Check if newer
    my @dat=split(/_/,$core);
***************
*** 100,110 ****
    my $v2=($#dat<2)? 1:pop @dat;
    my $version=$v2."_".$v1;
!  next unless ($current{$core}<$v1);
  next if (-e $core);
!  $ftp->cwd("$core")||die $@,$core;
   print "Working on $core\n";
   push @cores,$core;#Remember the DB names
   mkdir($core);
   chdir($core);
   my @files=grep (!/total/,$ftp->dir);
  my $cf=$ftp->pwd;
--- 96,114 ----
    my $v2=($#dat<2)? 1:pop @dat;
    my $version=$v2."_".$v1;
!   my $dbname=join('_',@dat);
!  next unless ($current{$dbname}<$version);
  next if (-e $core);
!  $ftp->cwd($core)||die $@,$core;
   print "Working on $core\n";
   push @cores,$core;#Remember the DB names
   mkdir($core);
   chdir($core);
+  
+ 
+   #$ftp->cwd($name)||die $name;
+   my @all=$ftp->dir;
+  foreach my $d (@all) {
+   
+ 
   my @files=grep (!/total/,$ftp->dir);
  my $cf=$ftp->pwd;
***************
*** 118,122 ****
     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; }
--- 122,126 ----
     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; }