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#!/usr/bin/perl
# Regression test driver for the primer3_core executable.
#
# For usage, see the usage statement in the code, below.
#
# ======================================================================
# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2010,
# 2011,2012,2016
# Whitehead Institute for Biomedical Research, Steve Rozen,
# Andreas Untergasser and Helen Skaletsky
# All rights reserved.
#
# This file is part of the primer3 suite.
#
# The primer3 suite is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later version.
#
# This software is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this file (file gpl-2.0.txt in the source distribution); if
# not, write to the Free Software Foundation, Inc., 51 Franklin St,
# Fifth Floor, Boston, MA 02110-1301 USA
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ======================================================================
use warnings 'all';
use strict;
use Cwd;
use Getopt::Long;
use POSIX; # For testing wait / system return value, e.g. WIFSIGNALED, WTERMSIG.....
use Config; # To get the number for SIGINT
sub perldiff($$);
sub test_fatal_errors();
sub main();
# Call system() with warnings turned off; needed for ActiveState / MS Windows.
sub _nowarn_system($);
our $def_executable = "../src/primer3_core";
our $exe = '../src/primer3_core';
our $set_files = '../test/';
our ($verbose, $do_valgrind, $do_valgrinda, $do_valgrindb, $return_action,
$winFlag, $fastFlag, $onetest);
our %signo;
our $valgrind_format;
# Global variable for Errors
my $all_ok;
# Create empty directories if needed
if (!(-d "../test/primer_list_tmp")) {
mkdir "../test/primer_list_tmp";
print "mkdir: ../test/primer_list_tmp\n";
}
if (!(-d "../test/primer1_list_tmp")) {
mkdir "../test/primer1_list_tmp";
print "mkdir: ../test/primer1_list_tmp\n";
}
if (!(-d "../test/primer1_th_list_tmp")) {
mkdir "../test/primer1_th_list_tmp";
print "mkdir: ../test/primer1_th_list_tmp\n";
}
if (!(-d "../test/th-w-other-tasks_list_tmp")) {
mkdir "../test/th-w-other-tasks_list_tmp";
print "mkdir: ../test/th-w-other-tasks_list_tmp\n";
}
main();
sub main() {
my %args;
# select STDERR;
$| = 1;
print "$0 for primer3_core version 2.6.1\n";
$all_ok = 1;
my $overall_start_time = time();
if (defined $Config{sig_name}) {
my $i = 0;
for my $name (split(' ', $Config{sig_name})) {
$signo{$name} = $i;
$i++;
}
}
# GetOptions handles various flag abbreviations and formats,
# such as -e ../src/primer3_core, --exe ../src/primer3_core,
# --exe=.../src/primer3_core
if (!GetOptions(\%args,
'valgrind',
'valgrinda',
'valgrindb',
'windows',
'fast',
'verbose',
'action',
'onetest=s',
'executable=s',
)) {
print "Usage: perl p3test.pl \\\n",
" [ --executable <primer3 executable> ] [ --onetest <test_name> ] ",
"[ --valgrind ] [ --verbose ] [ --action ] [ --windows ] [ --fast ]\n",
"\n",
" where <primer3 executable> defaults to ../src/primer3_core\n";
exit -1;
}
$exe = $args{'executable'} if defined$ args{'executable'};
$winFlag = defined $args{'windows'};
$verbose = defined $args{'verbose'};
$fastFlag = defined $args{'fast'};
$do_valgrind = $args{'valgrind'};
$do_valgrinda = $args{'valgrinda'};
$do_valgrindb = $args{'valgrindb'};
$return_action = $args{'action'};
if ($do_valgrinda || $do_valgrindb) {
$do_valgrind = 1;
}
if ($winFlag && $do_valgrind) {
print "$0: Cannot specify both --valgrind and --windows\n";
exit -1;
}
my $valgrind_exe = "/usr/bin/valgrind";
my $log_file_arg_for_valgrind = "--log-file-exactly";
if ($do_valgrind) {
if (!-x $valgrind_exe) {
print "Cannot find $valgrind_exe; will try `/usr/local/bin/valgrind`\n";
$valgrind_exe = "/usr/local/bin/valgrind";
}
if (!-x $valgrind_exe) {
print "Cannot find $valgrind_exe; will try `which valgrind`\n";
$valgrind_exe= `which valgrind`;
chomp($valgrind_exe);
if (!$valgrind_exe || ! -x $valgrind_exe) {
die "Cannot execute $valgrind_exe";
}
}
# Need to deal with different arguments in
# different version of valgrind
my $valgrind_version = `$valgrind_exe --version`;
if ($valgrind_version =~ /([0-9]+)\.([0-9]+)\./) {
if (($1 > 3) || (($1 == 3) && ($2 > 2))) {
$log_file_arg_for_valgrind = "--log-file";
}
}
}
$valgrind_format = $valgrind_exe
. " --leak-check=yes --show-reachable=yes " # --track-origins=yes
. "$log_file_arg_for_valgrind=%s.vg ";
if ($winFlag) {
$exe = '..\\src\\primer3_core.exe';
$set_files = '..\\test\\';
}
my $exit_stat = 0;
die "Cannot execute $exe" unless -x $exe;
print
"\n\n$0: testing $exe\n\n",
"START, ", scalar(localtime), "\n";
print "verbose mode\n" if $verbose;
print "valgrind mode\n" if $do_valgrind;
# Tests in %default_version2 use --default_version=2.
# Others use -default_version=1.
my %default_version2 = ('th-w-other-tasks' => 1,
'primer_thermod_align' => 1,
'primer_thermod_align_formatted' => 1,
'primer1_th' => 1,
'primer_mispriming_th' => 1,
'primer_must_use_th' => 1,
'primer_new_tasks_th' => 1,
'primer_task_th' => 1,
'primer_thal_args' => 1,
'primer_boundary' => 1, # Put the quickest tests first.
'primer3_v1_1_4_default_settings',
'primer3web_v0_4_0_default_settings',
'primer3web_v3_0_0_default_settings',
'primer3web_v4_0_0_default_settings',
'primer_overhang_th' => 1,
);
my @TESTS = (
# New tests that use new melting temperature
# and thermodynamic alignments
# Put the quickest tests first.
'primer_must_use_th',
'primer_sec_struct_dpal',
'primer_task_th',
'primer_thal_args',
'primer_thal_max_seq_error',
'primer_first_base_index',
'primer_must_match',
'test_compl_error',
'test_left_to_right_of_right',
'dv_conc_vs_dntp_conc',
'primer_boundary',
'primer_boundary1',
'primer_boundary_formatted',
'primer_boundary1_formatted',
'primer3_v1_1_4_default_settings',
'primer3web_v0_4_0_default_settings',
'primer3web_v3_0_0_default_settings',
'primer3web_v4_0_0_default_settings',
'primer_internal',
'primer_internal1',
'primer_internal_formatted',
'primer_internal1_formatted',
'primer_ok_regions',
'primer_ok_regions_formatted',
'primer_ok_regions2',
'primer_tm_lc_masking',
'primer_tm_lc_masking_formatted',
'primer_start_codon',
'primer_task',
'primer_task_formatted',
'primer_renewed_tasks',
'primer_dmso_formamide',
'primer_new_tasks',
'primer_new_tasks_formatted',
'primer_internal_position',
'primer_annealing_temp',
'primer_windows_newlines',
'primer_must_overlap_point',
'primer_overlap_junction',
'primer_all_settingsfiles',
'primer_high_tm_load_set',
'primer_high_gc_load_set',
'primer_gc_end',
'primer_check',
'primer_must_use',
'primer_must_use_formatted',
'primer_syntax',
'primer_end_pathology',
'primer_num_best',
'primer_quality_boundary',
'primer',
'primer1',
'primer_mispriming',
'primer_mispriming_formatted',
'primer_mispriming_boundary1',
'primer_mispriming_boundary1_formatted',
'primer_mispriming_boundary2',
'primer_mispriming_boundary2_formatted',
'primer_mispriming_long_lib',
'primer_rat',
'primer_human',
'long_seq',
'primer_position_penalty',
'primer_position_penalty_formatted',
'p3-tmpl-mispriming',
'primer_poly_x',
'primer_three_prime_distance',
'primer_obj_fn',
'p3_3_prime_n',
'primer_masker',
'primer_masker_formatted',
'primer_overhang',
# Put slow tests last
'primer_overhang_th',
'primer_mispriming_th',
'th-w-other-tasks',
'primer_new_tasks_th',
'primer_sec_struct_thal',
'primer_thermod_align',
'primer_thermod_align_formatted',
'primer1_th',
'primer_lib_amb_codes',
);
if (!$args{'onetest'}) {
test_fatal_errors();
} else {
@TESTS = $args{'onetest'};
}
# The range of this for loop is a set of test names
# that get translated into file names inside the loop.
for my $test (@TESTS) {
# We are inside the for loop here....
print "$test...";
my $test_start_time = time();
if ($fastFlag && (($test eq 'th-w-other-tasks')
|| ($test eq 'primer_obj_fn')
|| ($test eq 'primer1_th')
|| ($test eq 'primer_mispriming_th')
|| ($test eq 'primer_new_tasks_th')
|| ($test eq 'primer_thermod_align')
|| ($test eq 'primer_thermod_align_formatted'))) {
print "[skipped in fast mode]\n";
next;
}
if ($winFlag && (($test eq 'primer_masker')
|| ($test eq 'primer_masker_formatted'))) {
print "[PRIMER_MASK_TEMPLATE not supported on Windows]\n";
next;
}
if ($do_valgrinda && (($test eq 'primer1_th')
|| ($test eq 'primer_lib_amb_codes'))) {
print "[skipped in fast valgrind mode a]\n";
next;
}
if ($do_valgrindb && ($test ne 'primer1_th')
&& ($test ne 'primer_lib_amb_codes')) {
print "[skipped in fast valgrind mode b]\n";
next;
}
my $default_version;
if ($default_version2{$test}) {
$default_version = '--default_version=2';
} else {
$default_version = '--default_version=1';
}
if ($test eq 'primer_lib_amb_codes') {
if ($fastFlag) {
print "[skipped in fast mode]\n";
next;
}
print
"\nNOTE: this test takes _much_ longer than the others ",
"(5 to 20 minutes or more).\n",
"starting $test at ", scalar(localtime), "...";
}
my $valgrind_prefix
= $do_valgrind ? sprintf $valgrind_format, $test : '';
# Figure out what the files are called for a particular test
my $testx = $test;
$testx =~ s/_formatted$//;
my $input = $testx . '_input';
my $output = $test . '_output';
my $tmp = $test . '.tmp';
# Make sure that needed files are present and readable
die "Cannot read $input" unless -r $input;
die "Cannot read $output" unless -r $output;
my $r; # Return value for tests
my %list_test
= ('primer' => 1,
'primer1' => 1,
'primer1_th' => 1,
'th-w-other-tasks' => 1);
if (exists($list_test{$test})) {
# These tests generate primer lists, which
# need to be checked separately.
my $list_tmp = $test.'_list_tmp';
# We need to chdir below because primer3 puts the 'list' files
# in the current working directory.
# get a list of the files to remove (if any) in this directory
my @tempList = glob('./' . $test.'_list_tmp/*');
# delete them
for my $t (@tempList) {
unlink $t;
}
# go down into primer|primer1 list_tmp directory
if (!chdir $list_tmp) { die "chdir $list_tmp: $!\n" }
my $tmpCmd;
# generate the necc. files; If $winFlag is
# set, run command with Windows backslashes
# in path.
my $settings = '';
if ($winFlag) {
if ($test eq 'th-w-other-tasks') {
$settings = '--p3_settings ..\\th-w-other-tasks-settings.txt --echo_settings';
}
$tmpCmd = "..\\$exe $default_version --strict_tags $settings ../$input >../$tmp";
} else {
if ($test eq 'th-w-other-tasks') {
$settings = '--p3_settings ../th-w-other-tasks-settings.txt --echo_settings';
}
$tmpCmd = "$valgrind_prefix ../$exe $default_version --strict_tags $settings ../$input >../$tmp";
}
$r = _nowarn_system($tmpCmd);
# back to main directory
if (!chdir "../") {
die "chdir \"..\": $!\n"
}
} elsif ($test =~ /settings$/) {
my $cmd = "$valgrind_prefix$exe $default_version --strict_tags --p3_settings_file=../settings_files/$test.txt --echo <$input >$tmp";
$r = _nowarn_system($cmd);
} elsif ($test =~ /formatted$/) {
my $cmd = "$valgrind_prefix$exe $default_version --strict_tags --format_output <$input >$tmp";
$r = _nowarn_system($cmd);
} elsif ($test =~ /_load_set/) {
my $cmd = "$valgrind_prefix$exe $default_version --strict_tags --p3_settings_file=$set_files$test.set --echo <$input >$tmp";
$r = _nowarn_system($cmd);
} else {
my $cmd = "$valgrind_prefix$exe $default_version --strict_tags <$input >$tmp";
$r = _nowarn_system($cmd);
}
unless ($r == 0) {
$all_ok = 0;
print "NON-0 EXIT: $r [FAILED]\n";
$exit_stat = -1;
next;
}
$r = perldiff $output, $tmp;
print ((time() - $test_start_time), "s ");
if ($r == 0) {
print "[OK]\n";
} else {
$all_ok = 0;
print "[FAILED]\n";
$exit_stat = -1;
}
if (exists($list_test{$test})) {
# Special processing for tests that generate files containing
# primer lists.
my $list_tmp = $test.'_list_tmp';
my $list_last = $test.'_list_last';
if (!-r $list_last) {
print "Configuration error, $list_last does not exist or is not readable ";
$r = 1;
}
my @tempList = glob($list_last.'/*');
# do _file by file_ comparison within primer_list_last to primer_list_tmp
# since we are not using diff - diff used to do directory comparison
for my $t (@tempList) {
# sneakily get correct paths since glob of primer_list_last returns
# primer_list_last/filename_within_primer_list_last
my $regex = "[^/]+/";
$t=~ s/$regex//g;
if (perldiff $list_tmp."/".$t, $list_last."/".$t) {
$r = 1;
}
}
print $test. "_list_files...";
if ($r == 0) {
print "[OK]\n";
} else {
$all_ok = 0;
print "[FAILED]\n";
$exit_stat = -1;
}
}
} # End of long for loop, for my $test in (.....)
# ==================================================
# If we were running under valgrind to look for memory-related
# errors (reading uninitialized memory, writing off the end of
# an array, etc) or leaks, then we look through the valgrind
# logs to summarize errors and leaks.
if ($do_valgrind) {
# Assume this is Unix/Linux envrionment, so
# we have grep.
my $r = system "grep ERROR *.vg */*.vg | grep -v 'ERROR SUMMARY: 0 errors'";
if (!$r) { # !$r because grep returns 0 if something is found,
# and if something is found, we have a problem.
$all_ok = 0;
print "\nValgrind ERRORs found [FAILED]";
$exit_stat = -1;
}
$r = system "grep 'definitely lost' *.vg */*.vg | grep -v ' 0 bytes'";
if (!$r) {
$all_ok = 0;
print "\nValgrind LEAKSs found [WARNING]";
$exit_stat = -1;
}
$r = system "grep 'possibly lost' *.vg */*.vg | grep -v ' 0 bytes'";
if (!$r) {
$all_ok = 0;
print "\nValgrind LEAKSs found [WARNING]";
$exit_stat = -1;
}
}
print "\nTests in $0 ran for ", (time() - $overall_start_time), " s \(", ((time() - $overall_start_time)/60), " min\)\n";
print "\nDONE ", scalar(localtime), " ";
print $all_ok ? "Passed all tests - [OK]\n\n\n" : "At least one test failed - [FAILED]\n\n\n";
if ($all_ok != 1 ) {
$exit_stat = -1;
}
if ($return_action || $do_valgrinda || $do_valgrindb) {
exit $exit_stat;
} else {
exit 0; # Generally we want the testing to continue.
}
}
# Usage: perldiff("filename1", "filename2")
# Return 0 if no differences are found,
# othewise return 1;
sub perldiff($$) {
my ($f1, $f2) = @_;
open F1, $f1 or die "open $f1: $!";
open F2, $f2 or die "open $f2: $!";
my @f1 = <F1>;
my @f2 = <F2>;
# If different number of lines, return FAIL.
if (@f1 != @f2) {
print "\n Different number of lines;\n";
print " on command line in test directory run:\n";
print " diff $f1 $f2\n\n";
return 1;
}
# check for differences on the lines, themselves
my $linenumber = 0;
my $line_end_diff = 0;
# iterate using lines in file1
while (@f1) {
$linenumber++;
# get the lines from each respective file
my $l1 = shift @f1;
my $l2 = shift @f2;
my $l1_orig = $l1;
my $l2_orig = $l2;
# Handle the diff in empty_1.{out2,tmp2} due to
# different executable names.
if ($exe ne $def_executable && $l1 =~/^USAGE:\s+\S+/) {
$l1 =~ s/^USAGE:\s+\S+/USAGE: ... /i;
$l2 =~ s/^USAGE:\s+\S+/USAGE: ... /i;
if ($verbose) {
print "removing executable name from\n",
"$l1_orig\n$l2_orig\n";
}
}
# Remove everything up to and including the first
# colon, which removes the executable name.
# This substitution must follow the USAGE
# substitution, above
my $regex = "[^:]+:";
my $quoteexe = quotemeta($def_executable);
# Edit executable name
if ($exe ne $def_executable && ($l1 =~ /$quoteexe/ || $l2 =~ /$quoteexe/)) {
$l1 =~ s/$regex//g;
$l2 =~ s/$regex//g;
if ($verbose) {
print "removing <executable>: from\n",
"$l1_orig\n$l2_orig\n";
}
}
# Edit release number
if ($l1 ne $l2) {
if ($l1 =~ /(libprimer3|primer3) release \d+\.\d+\.\d+/
&& $l2 =~ /(libprimer3|primer3) release \d+\.\d+\.\d+/) {
$l1 =~ s/(libprimer3|primer3) release \d+\.\d+\.\d+//;
$l2 =~ s/(libprimer3|primer3) release \d+\.\d+\.\d+//;
}
}
# If this is the tag with the settings file path, replace \ by / to make it
# the same on both Linux and Windows
if ($l1 =~ /^P3_SETTINGS_FILE_USED/ && $l2 =~ /^P3_SETTINGS_FILE_USED/) {
$l1 =~ s/\\/\//g;
$l2 =~ s/\\/\//g;
}
$linenumber++;
# Check for difference between two edited lines (line by line)
if ($l1 ne $l2) {
print
"\n Difference found at line $linenumber:\n",
" < $l1_orig\n",
" > $l2_orig\n";
print " There may be additional differences.\n";
print " On command line in test directory run\n\n";
print " diff $f1 $f2\n\n";
return 1;
}
}
return 0;
}
sub test_fatal_errors() {
# Get all the files that match primer_global_err/*.in:
my @inputs = glob("./primer_global_err/*.in");
my $r;
my $fatal_error_problem = 0;
print "\ntesting fatal errors...\n";
my $output_and_err_tested = 0;
for (@inputs) {
my ($root) = /(.*)\.in$/; # Hint, the parens around $root give
# the result of the match in
# an array context.
print " $root\n";
my $valgrind_prefix
= $do_valgrind ? sprintf $valgrind_format, $root : '';
my $cmd;
if ($_ =~ /bad_settings\d\.in/) {
# For testing the settings files we need the
# names of tests and the settings to be parallel
$cmd = "$valgrind_prefix$exe --strict_tags --p3_settings_file $_ primer_global_err/input_for_settings_tests.txt > $root.tmp 2> $root.tmp2";
# print STDERR $cmd, "\n";
} else {
if ($output_and_err_tested) {
$cmd = "$valgrind_prefix$exe --strict_tags <$_ > $root.tmp 2> $root.tmp2";
} else {
# We need to test the -output and -error command line arguments plus
# simply taking the file name as an argument (no "<")
$cmd = "$valgrind_prefix$exe --strict_tags $_ --output $root.tmp --error $root.tmp2";
$output_and_err_tested = 1;
print "Testing --output and --error flags on\n$cmd\n";
}
}
$r = _nowarn_system($cmd);
if ($? == 0) {
my $r = $? >> 8;
print
"\nErroneous 0 exit status ($?) from command $cmd\n";
$fatal_error_problem = 1;
}
if (perldiff "$root.tmp", "$root.out") {
print
"Difference found between $root.out and $root.tmp\nfrom $cmd\n\n";
$fatal_error_problem = 1;
}
if (perldiff "$root.tmp2", "$root.out2") {
print
"\nDifference found between $root.out2 and $root.tmp2\nfrom $cmd\n\n";
$fatal_error_problem = 1;
}
}
if ($fatal_error_problem == 1){
$all_ok = 0;
}
print(($fatal_error_problem ? "[FAILED]" : "[OK]") ,"\n");
}
sub _nowarn_system($) {
my $cmd = shift;
if ($verbose) { print "\n$cmd\n" }
no warnings 'all';
my $r = system $cmd;
my $r2 = $?;
if (!$winFlag && WIFEXITED($r2)) {
$r = WEXITSTATUS($r2);
if (defined $signo{'INT'}) {
if ($r == $signo{'INT'}) {
print "\nCommand: $cmd\n";
print "generated exit value $r\n";
print "Presumably caused by catching SIGINT\n";
print "Tests halted\n\n";
print "\nWARNING: not all tests executed ... [FAILED]\n";
if (!$all_ok) {
print "\n\nIn addition, at least 1 test FAILED ... [FAILED]\n\n";
}
exit;
}
}
}
if (!$winFlag && WIFSIGNALED($r2)) {
my $r2 = WTERMSIG($r2);
print "Exited with signal $r2\n";
}
$r;
}
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