src/hg/utils/automation/SafePipe.pm 1.5

Index: src/hg/utils/automation/SafePipe.pm
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/SafePipe.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/utils/automation/SafePipe.pm	10 Mar 2009 18:35:37 -0000	1.4
+++ src/hg/utils/automation/SafePipe.pm	10 Mar 2009 19:27:47 -0000	1.5
@@ -1,112 +1,116 @@
 #
 # SafePipe class: a safe replacement for system; checks every command in a pipe for failure
 # (which is NOT possible with `` or system).
 #
 # We also capture stderr from all commands in a separate buffer.
 #
 # DO NOT EDIT the /cluster/bin/scripts copy of this file --
 # edit ~/kent/src/hg/utils/automation/SafePipe.pm instead.
 
 # $Id$
 
 package SafePipe;
 
 use warnings;
 use strict;
 
 sub new
 {
 # $args{CMDS} (required): list of commands
 # $args{STDOUT} (optional): file to use for stdout; if not provided, we copy text of stdout into the STDOUT field.
 # $args{STDERR} (optional): file to use for stderr; if not provided, we copy text of stderr into the STDERR field.
 # Files are useful if you want to leave the data on disk for later use.
 # Use STDOUT/STDERR  => '/dev/null' if you want to discard stdout/stderr.
     my ($class, %args) = (@_);
     die "$class: missing CMDS list" unless(defined($args{CMDS}) && ref($args{CMDS}) eq 'ARRAY');
     my $ref = {};
     $ref->{$_} = $args{$_} for (keys %args);
     bless $ref, $class;
     return $ref;
 }
 
 sub stderr
 {
 # returns text of STDERR from executed commands.
 # Use only if you did NOT provide a STDOUT file to the new method.
     my ($obj) = @_;
     return $obj->{STDERR};
 }
 
 sub stdout
 {
 # returns text of STDOUT from executed commands.
 # Use only if you did NOT provide a STDOUT file to the new method.
     my ($obj) = @_;
     return $obj->{STDOUT};
 }
 
 sub cmd
 {
 # returns text of executed command pipe (useful for debugging)
     my ($obj) = @_;
     return $obj->{CMD};
 }
 
 sub statuses
 {
 # returns list of statuses from executed command (useful if you want to
 # print very specific errors).
     my ($obj) = @_;
     return $obj->{STATUSES};
 }
 
 sub exec
 {
 # Exececute the pipe; returns sum of statuses, to facilitate quick test by caller
 # for success. Individual statuses are available via statuses method.
     my ($obj) = @_;
 
     my $stderrCreated = 0;
     my $stderrFile = $obj->{STDERR};
+    my $tmpDir = $ENV{TMPDIR} || "/data/tmp";
+    if(!(defined($tmpDir) && -d $tmpDir)) {
+        $tmpDir = "/tmp";
+    }
     if(!(defined($stderrFile))) {
-        $stderrFile = "/data/tmp/SafePipe$$.err";
+        $stderrFile = "$tmpDir/SafePipe$$.err";
         $stderrCreated = 1;
         unlink($stderrFile);
     }
     my $stdoutCreated = 0;
     my $stdoutFile = $obj->{STDOUT};
     if(!(defined($stdoutFile))) {
-        $stdoutFile = "/data/tmp/SafePipe$$.out";
+        $stdoutFile = "$tmpDir/SafePipe$$.out";
         $stdoutCreated = 1;
         unlink($stdoutFile);
     }
 
     my $cmd = join(" 2>> $stderrFile | ", @{$obj->{CMDS}});
     $cmd .= " > $stdoutFile 2>> $stderrFile; echo \${PIPESTATUS[@]}";
     $obj->{CMD} = $cmd;
     my $output = `$cmd`;
 
     # get individual statuses by parsing PIPESTATUS list
     my @list = split(/\s+/, $output);
     print STDERR "cmd: $cmd; output: $output\n" if($obj->{DEBUG});
     $obj->{STATUSES} = \@list;
     $obj->{SUM} = 0;
     $obj->{SUM} += abs for (@list);
 
     if($stderrCreated) {
         open(ERR, $stderrFile) || die "ERROR: Can't open stderr file \'$stderrFile\': $!\n";
         $obj->{STDERR} = join("", <ERR>);
         close(ERR);
         unlink($stderrFile);
     }
     if($stdoutCreated) {
         open(OUT, $stdoutFile) || die "ERROR: Can't open stdout file \'$stdoutFile\': $!\n";
         $obj->{STDOUT} = join("", <OUT>);
         close(OUT);
         unlink($stdoutFile);
     }
 
     return $obj->{SUM};
 }
 
 1;