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|
#!/usr/bin/perl -w
######################################################################
#
# Name: getprogramnames
#
# Description:
# Runs wossname to get the EMBOSS programs on the path
# together with their groups
#
# Args:
# *** These are all global variables ***
# %grpnames - hash of key=lowercase group name,
# value = uppercase group description
# %progs - hash of key=program name, value = program description
# %groups - hash of key=lowercase group name, value = program names
#
######################################################################
sub getprogramnames ( ) {
my $prog; # program name
my $capgrp; # uppcase group name
my $grp; # lowercase group name
open (PROGS, "wossname -noembassy -auto |") ||
die "Cannot run wossname";
while ($prog = <PROGS>) {
if ($prog =~ /^\s*$/) { # ignore blank lines
next;
} elsif ($prog =~ /^([A-Z0-9 ]+)$/) { # uppcase means a group name
$capgrp = $1;
$grp = lc($capgrp);
$grp =~ s/ +/_/g; # lowercase one-word group_name
$grpnames{$grp} = $capgrp;
# print "Group $grp = $capgrp\n";
} elsif ($prog =~ /^(\S+) +(.*)/) {
$progs{$1} = $2;
$groups{$grp} .= "$1 ";
# print "Program in $grp = $1\n";
}
}
close PROGS;
foreach $e(@embassylist) {
open (PROGS, "wossname -showembassy $e -auto |") ||
die "Cannot run wossname";
while ($prog = <PROGS>) {
if ($prog =~ /^\s*$/) { # ignore blank lines
next;
} elsif ($prog =~ /^([A-Z0-9 ]+)$/) { # uppcase means a group name
$capgrp = $1;
$grp = lc($capgrp);
$grp =~ s/ +/_/g; # lowercase one-word group_name
$grpnames{$grp} = $capgrp;
# print "Group $grp = $capgrp\n";
} elsif ($prog =~ /^(\S+) +(.*)/) {
$progs{$1} = $2;
$groups{$grp} .= "$1 ";
$embassyprogs{$1} = $e;
# print "Program in $grp = $1\n";
}
}
close PROGS;
}
}
@embassylist = ("appendixd",
"cbstools",
"clustalomega",
"domainatrix",
"domalign",
"domsearch",
"emnu",
"esim4",
"hmmer",
"hmmernew",
"iprscan",
"meme",
"memenew",
"mira",
"mse",
"myemboss", # we avoid documenting these examples
"myembossdemo", # we avoid documenting these examples
"phylip",
"phylipnew",
"signature",
"structure",
"topo",
"vienna", # old vienna
"vienna2",
);
%cmd = ();
%progs = ();
%embassyprogs = ();
$failtxt = "";
$leaktxt = "";
$errortxt = "";
$timetxt="";
$reachtxt = "";
$othertxt = "";
getprogramnames();
open (DAT, "../memtest.dat") || die "Cannot open file memtest.dat";
while (<DAT>) {
if (/^[\#]/) {next}
if (/^(\S+) = (.*)/) {$cmd{$1} = $2};
if (/^(\S+) =test= (.*)/) {$cmd{$1} = $2};
}
close DAT;
open (DAT, "qatestcmd.dat") || die "Cannot open file qatestcmd.dat";
while (<DAT>) {
if (/^[\#]/) {next}
if (/^(\S+) = (.*)/) {$cmd{$1} = $2};
if (/^(\S+) =test= (.*)/) {$cmd{$1} = $2};
}
close DAT;
while (<>) {
if (/^Valgrind time /) {next}
elsif (/^Valgrind test (\S+)/) {
$name = $1;
($appname) = ($name =~ /^([^-]+)/);
$isembassy = 0;
$embassy = "EMBOSS";
if(!defined($progs{$appname})) {
if(-e "/homes/pmr/check/bin/$appname")
{$embassy = "EMBOSSCHECK"}
else
{print "Unknown application '$appname'\n"}
}
elsif(defined($embassyprogs{$appname})) {
$isembassy = 1;
$embassy = $embassyprogs{$appname};
}
$leak = $status = 0;
if (/^Valgrind test (\S+) OK [\(]all clean[\)]/) {next}
elsif (/^Valgrind test (\S+) OK [\(]still reachable +([^\)]+)/) {
$status = $2;
$reachcnt{$embassy}++;
$reachtxt .= "\n";
$reachtxt .= "$name $embassy reachable $status\n";
$reachtxt .= "\% $cmd{$name}\n";
}
elsif (/^Valgrind test (\S+) (timed out)/) {
$status = $2;
$timecnt{$embassy}++;
$timetxt .= "\n";
$timetxt .= "$name $embassy status $status\n";
$timetxt .= "\% $cmd{$name}\n";
$timetxt .= "$txt";
}
elsif (/^Valgrind test (\S+) returned status (\d+)/) {
$status = $2;
$failcnt{$embassy}++;
$failtxt .= "\n";
$failtxt .= "$name $embassy status $status\n";
$failtxt .= "\% $cmd{$name}\n";
$failtxt .= "$txt";
}
elsif (/^Valgrind test (\S+) leak ([^e]+bytes)/) {
$leak = $2;
$leakcnt{$embassy}++;
$leak =~ s/\(possibly 0 \[0\]\) //;
$leaktxt .= "\n";
$leaktxt .= "$name $embassy leak $leak\n";
$leaktxt .= "\% $cmd{$name}\n";
}
elsif (/^Valgrind test (\S+) errors (\S+\s+\S+)/) {
$err = $2;
$errorcnt{$embassy}++;
$errortxt .= "\n";
$errortxt .= "$name $embassy ** errors ** $err\n";
$errortxt .= "\% $cmd{$name}\n";
}
elsif (/^Valgrind test (\S+) (.*)\n/) {
$msg = $2;
$othercnt{$embassy}++;
$othertxt .= "\n";
$othertxt .= "$name $embassy ++ '$msg'\n";
$othertxt .= "\% $cmd{$name}\n";
}
$txt = "";
}
else {$txt .= $_}
}
if($failtxt ne "") {
print "\nFailed\n======\n";
foreach $e(sort(keys(%failcnt))) {
printf " %3d %s\n", $failcnt{$e}, $e;
}
print "$failtxt\n";
}
if($errortxt ne "") {
print "\nErrors\n======\n";
foreach $e(sort(keys(%errorcnt))) {
printf " %3d %s\n", $errorcnt{$e}, $e;
}
print "$errortxt\n";
}
if($timetxt ne "") {
print "\nTimed out\n========\n";
foreach $e(sort(keys(%timecnt))) {
printf " %3d %s\n", $timecnt{$e}, $e;
}
print "$timetxt\n";
}
if($othertxt ne "") {
print "\nOther problems\n==============\n";
foreach $e(sort(keys(%othercnt))) {
printf " %3d %s\n", $othercnt{$e}, $e;
}
print "$othertxt\n";
}
if($leaktxt ne "") {
print "\nLeaks\n=====\n";
foreach $e(sort(keys(%leakcnt))) {
printf " %3d %s\n", $leakcnt{$e}, $e;
}
print "$leaktxt\n";
}
if($reachtxt ne "") {
print "\nReachable\n=========\n";
foreach $e(sort(keys(%reachcnt))) {
printf " %3d %s\n", $reachcnt{$e}, $e;
}
print "$reachtxt\n";
}
|
