[Cogs-guts] ensupdate load_ensembl.pl,1.6,1.7

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

Update of /cvsroot/cogs/ensupdate
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv10744

Modified Files:
	load_ensembl.pl 
Log Message:
Overflow system implemented

Index: load_ensembl.pl
===================================================================
RCS file: /cvsroot/cogs/ensupdate/load_ensembl.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** load_ensembl.pl	14 Sep 2007 18:04:55 -0000	1.6
--- load_ensembl.pl	9 Jan 2008 20:09:42 -0000	1.7
***************
*** 1,3 ****
! #!/usr/bin/perl
  use DBI;
  
--- 1,3 ----
! #!/stf/sys/bin/perl
  use DBI;
  
***************
*** 16,20 ****
  my $msqldir=$ENV{MYSQL_DATA};
  open (MSQLV,'mysql -V|')||die 'Mysql crashed or no mysql installed';
- if ($overfl) { $avail=check_for_overflow($msqldir) ; }
  my $msqlv=<MSQLV>;
  close MSQLV;
--- 16,19 ----
***************
*** 27,30 ****
--- 26,30 ----
  $cs .= "port=$port;" if ($port);
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
+ $dbh->{mysql_auto_reconnect}=1;
  #Special table with every DB that loads, should be created in advance
  
***************
*** 50,53 ****
--- 50,55 ----
    my $dbname=join('_', @ver);
    my ($obsol)=grep(/$dbname/,@dbs);
+   my $ifed=$dbh->prepare("drop database  if exists $db") ||die "Couldn't create DB $db\n"; #Should we check first and drop it if exists?
+   $ifed->execute||die;
    my $str=$dbh->prepare("create database $db") ||die "Couldn't create DB $db\n"; #Should we check first and drop it if exists?
    my $list=$dbh->prepare("insert into ens_dbnames (db_name, version,current) values (?,?,'yes')") ||die "Couldn't prepare- recording the DB list\n",$DBI::errstr;
***************
*** 62,71 ****
    $up=$pass ? "-u $user -p$pass " : "-u $user";
    my $sarg="mysql -h $host $up $db <$ddlfile";
!   my $avail;
!   if ($overfl) { $avail=check_for_overflow($msqldir) ; }
    if (($avail<25)&&($msqldir)) {
! 	  print "Using $overfl overflow\n";
! 	  system("mv $msqldir/$db $overfl")==0||die "Could not move to $overfl $?:$!";
! 	  system("ln -s $overfl/$db $msqldir")==0||die "Could not move to $overfl $?:$!";
    }
    print "$sarg\n";
--- 64,74 ----
    $up=$pass ? "-u $user -p$pass " : "-u $user";
    my $sarg="mysql -h $host $up $db <$ddlfile";
!   my ($avail,$next);
! if ($overfl) { ($avail,$next)=check_for_overflow($msqldir,$overfl) ; }
    if (($avail<25)&&($msqldir)) {
! 	  die "No space left on original device and in overflow devices (if defined), cannot continue" unless ($next);
! 	  print "Using $overfl $next\n";
! 	  system("mv $msqldir/$db $next")==0||die "Could not move to $overfl $?:$!";
! 	  system("ln -s $next/$db $msqldir")==0||die "Could not move to $overfl $?:$!";
    }
    print "$sarg\n";
***************
*** 78,81 ****
--- 81,91 ----
    system($load)==0||die"Couldn't import\n$load\n";
    }
+     open (DATF, "ls *.txt| wc -l|")||die;
+   my $cntd=<DATF>;
+   close DATF;
+   if ($cntd>0) {
+   my $load="mysqlimport -L -h $host  $up $db *.txt";
+   system($load)==0||die"Couldn't import\n$load\n";
+   }
   $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
    if ($obsol) {
***************
*** 99,105 ****
  
  sub check_for_overflow {
! my $storage=shift;
! unless ($storage) { die "Do not know where to overflow to, see that environment var MYSQL_DATA is set"; }
! open (SZ,"df -h $storage|")||die "$?:$!";
  my $head=<SZ>;
  my $where=<SZ>;
--- 109,114 ----
  
  sub check_for_overflow {
! my $default=shift;
! open (SZ,"df -h $default|")||die "$?:$!";
  my $head=<SZ>;
  my $where=<SZ>;
***************
*** 107,113 ****
  $dat=~s/^[\s\t]+//;
  my ($size,$used,$avail,$mount)=split(/[\t\s]+/,$dat);
! unless ($avail=~/G$/) { return 0};
! $avail=~s/\D//g;
! return $avail;
  }
  
--- 116,140 ----
  $dat=~s/^[\s\t]+//;
  my ($size,$used,$avail,$mount)=split(/[\t\s]+/,$dat);
! if ($avail=~/G$/) { 
! 	$avail=~s/\D//g;
! 	return $avail,undef if ($avail>20);
! }
! my $disks=shift;
! unless ($disks) { die "Do not know where to overflow to, see that environment var MYSQL_DATA is set"; }
! my @storage=split(/:/,$disks);
! my $next;
! foreach my $storage (@storage) {
! open (SZ,"df -h $storage|")||die "$?:$!";
! my $head=<SZ>;
! #my $where=<SZ>;
! my $dat=<SZ>;
! $dat=~s/^[\s\t]+//;
! my ($fs,$size,$used,$availnext,$mount)=split(/[\t\s]+/,$dat);
! unless ($availnext=~/G$/) { next };
! $availnext=~s/\D//g;
! if ($availnext>20) { $next=$storage;}
! }
! 
! return $avail,$next;
  }