[Cogs-guts] ensupdate load_ensembl.pl,1.5,1.6

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

Update of /cvsroot/cogs/ensupdate
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv13804

Modified Files:
	load_ensembl.pl 
Log Message:
added mysql connect params, overflow, bugs

Index: load_ensembl.pl
===================================================================
RCS file: /cvsroot/cogs/ensupdate/load_ensembl.pl,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** load_ensembl.pl	12 Dec 2005 14:29:42 -0000	1.5
--- load_ensembl.pl	14 Sep 2007 18:04:55 -0000	1.6
***************
*** 6,16 ****
  my $drop=shift;
  my $clean=shift;
! chdir($locdir);
  my (%db,@dbs);
  my $user=$ENV{ENS_ADMIN};
! my $pass=$ENV{ENS_PASS};
  my $host=$ENV{ENS_HOST};
  my $sock=$ENV{ENS_SOCK};
  open (MSQLV,'mysql -V|')||die 'Mysql crashed or no mysql installed';
  my $msqlv=<MSQLV>;
  close MSQLV;
--- 6,20 ----
  my $drop=shift;
  my $clean=shift;
! chdir($locdir)||die $locdir;
  my (%db,@dbs);
  my $user=$ENV{ENS_ADMIN};
! my $pass=$ENV{ENS_ADMINPASS};
  my $host=$ENV{ENS_HOST};
  my $sock=$ENV{ENS_SOCK};
+ my $port=$ENV{ENS_PORT};
+ my $overfl=$ENV{ENS_OVERFLOW};
+ 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;
***************
*** 21,29 ****
  my $cs = "dbi:mysql:database=$sid;host=$host;";
  $cs .= "mysql_socket=$sock;" if ($sock);
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
  #Special table with every DB that loads, should be created in advance
! my $chdb=$dbh->prepare("use ensembl_databases")||die "Couldn't prepare- recording the DB\n";
! 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;
! my $updatec=$dbh->prepare("update ens_dbnames set current='no' where db_name=?") ||die "Couldn't prepare- recording the DB list\n",$DBI::errstr;
  	my $droplist=$dbh->prepare("select db_name from ens_dbnames where current='yes'") ||die "Couldn't prepare- reading the DB list\n",$DBI::errstr;
  	$droplist->execute;
--- 25,33 ----
  my $cs = "dbi:mysql:database=$sid;host=$host;";
  $cs .= "mysql_socket=$sock;" if ($sock);
+ $cs .= "port=$port;" if ($port);
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
  #Special table with every DB that loads, should be created in advance
! 
! 
  	my $droplist=$dbh->prepare("select db_name from ens_dbnames where current='yes'") ||die "Couldn't prepare- reading the DB list\n",$DBI::errstr;
  	$droplist->execute;
***************
*** 47,61 ****
    my ($obsol)=grep(/$dbname/,@dbs);
    my $str=$dbh->prepare("create database $db") ||die "Couldn't create DB $db\n"; #Should we check first and drop it if exists?
    $chdb->execute ||die $DBI::errstr,"\n";
    $str->execute ||die  "Couldn't create DB $db\n ",$DBI::errstr;
    $list->execute($db,$ver) ||die "Couldn't record the database\n",$DBI::errstr;
    chdir($db);
    system('pwd');
    my $ddlfile=($majormver<5)?"$db.mysql40_compatible.sql":"$db.sql";
!   my $sarg="mysql -h $host -u $user -p$pass $db <$ddlfile";
    print "$sarg\n";
    system($sarg)==0 ||die "Failed to create schema for $db\n";
!   my $load="mysqlimport -L -h $host -u $user -p$pass $db *.txt.table";
!   system($load)==0||die"Couldn't import\n";
   $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
    if ($obsol) {
--- 51,81 ----
    my ($obsol)=grep(/$dbname/,@dbs);
    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;
+   my $chdb=$dbh->prepare("use ensembl_databases")||die "Couldn't prepare- recording the DB\n";
    $chdb->execute ||die $DBI::errstr,"\n";
    $str->execute ||die  "Couldn't create DB $db\n ",$DBI::errstr;
    $list->execute($db,$ver) ||die "Couldn't record the database\n",$DBI::errstr;
+   my $updatec=$dbh->prepare("update ens_dbnames set current='no' where db_name=?") ||die "Couldn't prepare- recording the DB list\n",$DBI::errstr;
    chdir($db);
    system('pwd');
    my $ddlfile=($majormver<5)?"$db.mysql40_compatible.sql":"$db.sql";
!   $up=$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 "$sarg\n";
    system($sarg)==0 ||die "Failed to create schema for $db\n";
!   open (DATF, "ls *.txt.table| wc -l|")||die;
!   my $cntd=<DATF>;
!   close DATF;
!   if ($cntd>0) {
!   my $load="mysqlimport -L -h $host  $up $db *.txt.table";
!   system($load)==0||die"Couldn't import\n$load\n";
!   }
   $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
    if ($obsol) {
***************
*** 77,78 ****
--- 97,113 ----
  close DBS;
  print "$count databases loaded successfully\n";
+ 
+ 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>;
+ my $dat=<SZ>;
+ $dat=~s/^[\s\t]+//;
+ my ($size,$used,$avail,$mount)=split(/[\t\s]+/,$dat);
+ unless ($avail=~/G$/) { return 0};
+ $avail=~s/\D//g;
+ return $avail;
+ }
+