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Summary

Bio::Root::Test - A common base for all Bioperl test scripts.

Package variables

Included modules

Inherit

Test::Builder::Module

Synopsis

  use lib '.'; # (for core package tests only)
  use Bio::Root::Test;

  test_begin(-tests => 20,
             -requires_modules => [qw(IO::String XML::Parser)],
             -requires_networking => 1);

  my $do_network_tests = test_network();
  my $output_debugging = test_debug();
  
  # Bio::Root::Test rewraps Test::Most, so one can carry out tests with
  # Test::More, Test::Exception, Test::Warn, Test::Deep, Test::Diff syntax

  SKIP: {
    # these tests need version 2.6 of Optional::Module to work
    test_skip(-tests => 10, -requires_module => 'Optional::Module 2.6');
    use_ok('Optional::Module');

    # 9 other optional tests that need Optional::Module
  }

  SKIP: {
    test_skip(-tests => 10, -requires_networking => 1);

    # 10 optional tests that require internet access (only makes sense in the
    # context of a script that doesn't use -requires_networking in the call to
    # &test_begin)
  }

  # in unix terms, we want to test with a file t/data/input_file.txt
  my $input_file = test_input_file('input_file.txt');

  # we want the name of a file we can write to, that will be automatically
  # deleted when the test script finishes
  my $output_file = test_output_file();

  # we want the name of a directory we can store files in, that will be
  # automatically deleted when the test script finishes
  my $output_dir = test_output_dir();

Description

This provides a common base for all BioPerl test scripts. It safely handles the
loading of Test::Most, itself a simple wrapper around several highly used test
modules: Test::More, Test::Exception, Test::Warn, Test::Deep, and Test::Diff. It
also presents an interface to common needs such as skipping all tests if
required modules aren't present or if network tests haven't been enabled. See
test_begin().
In the same way, it allows you to skip just a subset of tests for those same
reasons, in addition to requiring certain executables and environment variables.
See test_skip().
It also has two further methods that let you decide if network tests should be
run, and if debugging information should be printed. See test_network() and
test_debug().
Finally, it presents a consistent way of getting the path to input and output
files. See test_input_file(), test_output_file() and test_output_dir().

Methods

Methods description

 Title   : test_begin
 Usage   : test_begin(-tests => 20);
 Function: Begin your test script, setting up the plan (skip all tests, or run
           them all)
 Returns : True if tests should be run.
 Args    : -tests               => int (REQUIRED, the number of tests that will
                                        be run)
           -requires_modules    => []  (array ref of module names that are
                                        required; if any don't load, all tests
                                        will be skipped. To specify a required
                                        version of a module, include the version
                                        number after the module name, separated
                                        by a space)
           -requires_module     => str (as above, but for just one module)
           -requires_networking => 1|0 (default 0, if true all tests will be
                                        skipped if network tests haven't been
                                        enabled in Build.PL)
           -requires_email      => 1   (if true the desired number of tests will
                                        be skipped if either network tests
                                        haven't been enabled in Build.PL or an
                                        email hasn't been entered)
           -excludes_os         => str (default none, if OS suppied, all tests
                                        will skip if running on that OS (eg.
                                        'mswin'))
           -framework           => str (default 'Test::Most', the Test module
                                        to load. NB: experimental, avoid using)

           Note, supplying -tests => 0 is possible, allowing you to skip all
           tests in the case that a test script is testing deprecated modules
           that have yet to be removed from the distribution

 Title   : test_skip
 Usage   : SKIP: {
                   test_skip(-tests => 10,
                             -requires_module => 'Optional::Module 2.01');
                   # 10 tests that need v2.01 of Optional::Module
           }
 Function: Skip a subset of tests for one of several common reasons: missing one
           or more optional modules, network tests haven't been enabled, a
           required binary isn't present, or an environmental variable isn't set
 Returns : n/a
 Args    : -tests               => int (REQUIRED, the number of tests that are
                                        to be skipped in the event one of the
                                        following options isn't satisfied)
           -requires_modules    => []  (array ref of module names that are
                                        required; if any don't load, the desired
                                        number of tests will be skipped. To
                                        specify a required version of a module,
                                        include the version number after the
                                        module name, separated by a space)
           -requires_module     => str (as above, but for just one module)
           -requires_executable => Bio::Tools::Run::WrapperBase instance
                                       (checks WrapperBase::executable for the
                                        presence of a binary, skips if absent)
           -requires_env        => str (checks %ENV for a specific env. variable,
                                        skips if absent)
           -excludes_os         => str (default none, if OS suppied, desired num
                                        of tests will skip if running on that OS
                                        (eg. 'mswin'))
           -requires_networking => 1   (if true the desired number of tests will
                                        be skipped if network tests haven't been
                                        enabled in Build.PL)
           -requires_email      => 1   (if true the desired number of tests will
                                        be skipped if either network tests
                                        haven't been enabled in Build.PL or an
                                        email hasn't been entered)

 Title   : test_output_file
 Usage   : my $output_file = test_output_file();
 Function: Get the full path of a file suitable for writing to.
           When your test script ends, the file will be automatically deleted.
 Returns : string (file path)
 Args    : none

 Title   : test_output_dir
 Usage   : my $output_dir = test_output_dir();
 Function: Get the full path of a directory suitable for storing temporary files
           in.
           When your test script ends, the directory and its contents will be
           automatically deleted.
 Returns : string (path)
 Args    : none

 Title   : test_input_file
 Usage   : my $input_file = test_input_file();
 Function: Get the path of a desired input file stored in the standard location
           (currently t/data), but correct for all platforms.
 Returns : string (file path)
 Args    : list of strings (ie. at least the input filename, preceded by the
           names of any subdirectories within t/data)
           eg. for the file t/data/in.file pass 'in.file', for the file
           t/data/subdir/in.file, pass ('subdir', 'in.file')

 Title   : test_network
 Usage   : my $do_network_tests = test_network();
 Function: Ask if network tests should be run.
 Returns : boolean
 Args    : none

 Title   : test_email
 Usage   : my $do_network_tests = test_email();
 Function: Ask if email address provided
 Returns : boolean
 Args    : none

 Title   : test_debug
 Usage   : my $output_debugging = test_debug();
 Function: Ask if debugging information should be output.
 Returns : boolean
 Args    : none

 Title   : float_is
 Usage   : float_is($val1, $val2);
 Function: test two floating point values for equality
 Returns : Boolean based on test (can use in combination with diag)
 Args    : two scalar values (floating point numbers) (required via prototype)
           test message (optional)

Methods code

sub Test::Warn::_canonical_got_warning {

        my ($called_from, $msg) = @_;
        my $warn_kind = $called_from eq 'Carp' ? 'carped' : ($called_from =~ /Bio::/ ? 'Bioperl' : 'warn');
        
        my $warning;
        if ($warn_kind eq 'Bioperl') {
            ($warning) = $msg =~ /\n--------------------- WARNING ---------------------\nMSG: (.+)\n---------------------------------------------------\n$/m;
            $warning ||= $msg; # shouldn't ever happen
        }
        else {
            my @warning_stack = split /\n/, $msg;   # some stuff of uplevel is included
            $warning = $warning_stack[0];
        }
        
        return {$warn_kind => $warning}; # return only the real message

}

sub Test::Warn::_diag_found_warning {

        foreach (@_) {
            if (ref($_) eq 'HASH') {
                ${$_}{carped} ? $Tester->diag("found carped warning: ${$_}{carped}")
                              : (${$_}{Bioperl} ? $Tester->diag("found Bioperl warning: ${$_}{Bioperl}")
                                 : $Tester->diag("found warning: ${$_}{warn}"));
            } else {
                $Tester->diag( "found warning: $_" );
            }
        }
        $Tester->diag( "didn't find a warning" ) unless @_;

}

sub Test::Warn::_cmp_got_to_exp_warning {

        my ($got_kind, $got_msg) = %{ shift() };
        my ($exp_kind, $exp_msg) = %{ shift() };
        return 0 if ($got_kind eq 'warn') && ($exp_kind eq 'carped');
        
        my $cmp;
        if ($got_kind eq 'Bioperl') {
            $cmp = $got_msg =~ /^\Q$exp_msg\E$/;
        }
        else {
            $cmp = $got_msg =~ /^\Q$exp_msg\E at \S+ line \d+\.?$/;
        }
        
        return $cmp;
    }
}

our @EXPORT = (@Test::Most::EXPORT,
               #@Bio::Root::Test::Warn::EXPORT,
               # Test::Warn method wrappers
               
               # BioPerl-specific
               qw(
                test_begin
                test_skip
                test_output_file
                test_output_dir
                test_input_file
                test_network
                test_email
                test_debug
                float_is
             ));

our $GLOBAL_FRAMEWORK = 'Test::Most';
our @TEMP_FILES;

}

sub test_begin {

    my ($skip_all, $tests, $framework) = _skip(@_);
    $GLOBAL_FRAMEWORK = $framework;

    if ($framework eq 'Test::Most') {
        # ideally we'd delay loading Test::Most until this point, but see BEGIN
        # block

        if ($skip_all) {
            eval "plan skip_all => '$skip_all';";
        }
        elsif (defined $tests && $tests == 0) {
            eval "plan skip_all => 'All tests are being skipped, probably because the module(s) being tested here are now deprecated';";
        }
        elsif ($tests) {
            eval "plan tests => $tests;";
        }

        return 1;
    }
    # go ahead and add support for other frameworks here
    else {
        die "Only Test::Most is supported at the current time\n";
    }

    return 0;

}

sub test_skip {

    my ($skip, $tests, $framework) = _skip(@_);
    $tests || die "-tests must be a number greater than 0";

    if ($framework eq 'Test::Most') {
        if ($skip) {
            eval "skip('$skip', $tests);";
        }
    }
    # go ahead and add support for other frameworks here
    else {
        die "Only Test::Most is supported at the current time\n";
    }

}

sub test_output_file {

    die "test_output_file takes no args\n" if @_;

    # RT 48813
    my $tmp = File::Temp->new();
    push(@TEMP_FILES, $tmp);
    close($tmp); # Windows needs this
    return $tmp->filename;

}

sub test_output_dir {

    die "test_output_dir takes no args\n" if @_;

    return tempdir(CLEANUP => 1);

}

sub test_input_file {

    return File::Spec->catfile('t', 'data', @_);

}

sub test_network {

    require Module::Build;
    my $build = Module::Build->current();
    return $build->notes('network');

}

sub test_email {

    require Module::Build;
    my $build = Module::Build->current();
    # this should not be settable unless the network tests work
    return $build->notes('email');

}

sub test_debug {

    return $ENV{'BIOPERLDEBUG'} || 0;

}

sub float_is {

($$;$) {    my ($val1, $val2, $message) = @_;
    # catch any potential undefined values and directly compare
    if (!defined $val1 || !defined $val2) {
        is($val1, $val2 ,$message);
    } else {
        is(sprintf("%g",$val1), sprintf("%g",$val2),$message);
    }
}

# decide if should skip and generate skip message

}

sub _skip {

    my %args = @_;

    # handle input strictly
    my $tests = $args{'-tests'};
    #(defined $tests && $tests =~ /^\d+$/) || die "-tests must be supplied and be an int\n";
    delete $args{'-tests'};

    my $req_mods = $args{'-requires_modules'};
    delete $args{'-requires_modules'};
    my @req_mods;
    if ($req_mods) {
        ref($req_mods) eq 'ARRAY' || die "-requires_modules takes an array ref\n";
        @req_mods = @{$req_mods};
    }
    my $req_mod = $args{'-requires_module'};
    delete $args{'-requires_module'};
    if ($req_mod) {
        ref($req_mod) && die "-requires_module takes a string\n";
        push(@req_mods, $req_mod);
    }

    my $req_net = $args{'-requires_networking'};
    delete $args{'-requires_networking'};

    my $req_email = $args{'-requires_email'};
    delete $args{'-requires_email'};

    my $req_env = $args{'-requires_env'};
    delete $args{'-requires_env'};

    # strip any leading $ in case someone passes $FOO instead of 'FOO'
    $req_env =~ s{^\$}{} if $req_env;

    my $req_exe = $args{'-requires_executable'};
    delete $args{'-requires_executable'};

    if ($req_exe && (!ref($req_exe) || !$req_exe->isa('Bio::Tools::Run::WrapperBase'))) {
        die "-requires_exe takes an argument of type Bio::Tools::Run::WrapperBase";
    }

    my $os = $args{'-excludes_os'};
    delete $args{'-excludes_os'};

    my $framework = $args{'-framework'} || $GLOBAL_FRAMEWORK;
    delete $args{'-framework'};

    # catch user mistakes
    while (my ($key, $val) = each %args) {
        die "unknown argument '$key' supplied, did you mistake 'required...' for 'requires...'?\n";
    }

    # test user requirments and return
    if ($os) {
        if ($^O =~ /$os/i) {
            return ('Not compatible with your Operating System', $tests, $framework);
        }
    }

    foreach my $mod (@req_mods) {
        my $skip = _check_module($mod);
        if ($skip) {
            return ($skip, $tests, $framework);
        }
    }

    if ($req_net && ! test_network()) {
        return ('Network tests have not been requested', $tests, $framework);
    }

    if ($req_email && ! test_email()) {
        return ('Valid email not provided; required for tests', $tests, $framework);
    }

    if ($req_exe) {
        eval {$req_exe->executable};
        if ($@) {
            my $msg = 'Required executable for '.ref($req_exe).' is not present';
            diag($msg);
            return ($msg, $tests, $framework);
        }
    }

    if ($req_env && !exists $ENV{$req_env}) {
        my $msg = 'Required environment variable $'.$req_env. ' is not set';
        diag($msg);
        return ($msg, $tests, $framework);
    }

    return ('', $tests, $framework);

}

sub _check_module {

    my $mod = shift;

    my $desired_version;
    if ($mod =~ /(\S+)\s+(\S+)/) {
        $mod = $1;
        $desired_version = $2;
    }

    eval "require $mod;";

    if ($@) {
	if ($@ =~ /Can't locate/) {
	    return "The optional module $mod (or dependencies thereof) was not installed";
	}
	else {
	    return "The optional module $mod generated the following error:\n $@";
	}
    }
    elsif ($desired_version) {
        no strict 'refs';
        unless (defined ${"${mod}::VERSION"}) {
            return "The optional module $mod didn't have a version, but we want v$desired_version";
        }
        elsif (${"${mod}::VERSION"} < $desired_version) {
            return "The optional module $mod was out of date (wanted v$desired_version)";
        }
    }

    return;
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  https://redmine.open-bio.org/projects/bioperl/

Email bix@sendu.me.uk

Chris Fields cjfields at bioperl dot org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _