comparison Roary/t/lib/TestHelper.pm @ 0:c47a5f61bc9f draft

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0:c47a5f61bc9f

package TestHelper;
use Moose::Role;
use Test::Most;
use Data::Dumper;
use File::Slurper qw(read_lines read_text);
use Test::Files;
use Test::Output;

$ENV{PATH} .= ":./bin";

sub compare_files {
    my ( $actual_file, $expected_file, $comment ) = @_;
    my @actual_lines   = sort( read_lines($actual_file) );
    my @expected_lines = sort( read_lines($expected_file) );
    is_deeply( \@actual_lines, \@expected_lines, $comment );
}

sub compare_groups_files {
    my ( $actual_file, $expected_file, $comment ) = @_;
    my @actual_lines   = sort( read_lines($actual_file) );
    my @expected_lines = sort( read_lines($expected_file) );

    my @actual_sorted_lines;
    for my $line (@actual_lines) {
        my @line_details = split( / /, $line );
        shift @line_details;
        my @sorted = sort(@line_details);
        push( @actual_sorted_lines, \@sorted );
    }

    my @expected_sorted_lines;
    for my $line (@expected_lines) {
        my @line_details = split( / /, $line );
        shift @line_details;
        my @sorted = sort(@line_details);
        push( @expected_sorted_lines, \@sorted );
    }
    is_deeply( \@actual_sorted_lines, \@expected_sorted_lines, $comment );
}


sub stdout_should_have
{
	my ( $script_name, $parameters, $expected ) = @_;
	my @input_args = split( " ", $parameters );
	open OLDERR, '>&STDERR';
	eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDERR;
        open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
	    stdout_like { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
        close STDERR;
    }
    open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
    close OLDERR or die "Can't close OLDERR: $!";
}


sub stdout_should_not_have
{
	my ( $script_name, $parameters, $expected ) = @_;
	my @input_args = split( " ", $parameters );
	open OLDERR, '>&STDERR';
	eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDERR;
        open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
	    stdout_unlike { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
        close STDERR;
    }
    open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
    close OLDERR or die "Can't close OLDERR: $!";
}



sub stderr_should_not_have
{
	my ( $script_name, $parameters, $expected ) = @_;
	my @input_args = split( " ", $parameters );
	open OLDOUT, '>&STDOUT';
	eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDOUT;
        open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
	    stderr_unlike { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
        close STDOUT;
    }
    open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
    close OLDOUT or die "Can't close OLDOUT: $!";
}

sub stderr_should_have
{
	my ( $script_name, $parameters, $expected ) = @_;
	my @input_args = split( " ", $parameters );
	open OLDOUT, '>&STDOUT';
	eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDOUT;
        open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
	    stderr_like { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
        close STDOUT;
    }
    open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
    close OLDOUT or die "Can't close OLDOUT: $!";
}


sub mock_execute_script_and_check_output {
    my ( $script_name, $scripts_and_expected_files, $columns_to_exclude ) = @_;

    system('touch empty_file');

    open OLDOUT, '>&STDOUT';
    open OLDERR, '>&STDERR';
    eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDOUT;
        open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
        local *STDERR;
        open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";

        for my $script_parameters ( sort keys %$scripts_and_expected_files ) {
            my $full_script = $script_parameters;
            my @input_args = split( " ", $full_script );

            my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
            eval($cmd);
            warn $@ if $@;

            my $actual_output_file_name   = $scripts_and_expected_files->{$script_parameters}->[0];
            my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
            ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name  $script_parameters" );
            if ( defined($columns_to_exclude) ) {
                is(
                    _exclude_variable_columns_from_spreadsheet( $actual_output_file_name,   $columns_to_exclude ),
                    _exclude_variable_columns_from_spreadsheet( $expected_output_file_name, $columns_to_exclude ),
                    'Actual and expected match output excluding variable columns'
                );
            }
            else {
                compare_ok( $actual_output_file_name, $expected_output_file_name,
                    "Actual and expected output match for '$script_parameters'" );

            }
            unlink($actual_output_file_name);
        }
        close STDOUT;
        close STDERR;
    }

    # Restore stdout.
    open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
    open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";

    # Avoid leaks by closing the independent copies.
    close OLDOUT or die "Can't close OLDOUT: $!";
    close OLDERR or die "Can't close OLDERR: $!";
    unlink('empty_file');
}

sub mock_execute_script_and_check_output_sorted_groups {
    my ( $script_name, $scripts_and_expected_files, $columns_to_exclude ) = @_;

    system('touch empty_file');

    open OLDOUT, '>&STDOUT';
    open OLDERR, '>&STDERR';
    eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDOUT;
        open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
        local *STDERR;
        open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";

        for my $script_parameters ( sort keys %$scripts_and_expected_files ) {
            my $full_script = $script_parameters;
            my @input_args = split( " ", $full_script );

            my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
            eval($cmd);
            warn $@ if $@;

            my $actual_output_file_name = $scripts_and_expected_files->{$script_parameters}->[0];

            my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
            ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name  $script_parameters" );
            if ( defined($columns_to_exclude) ) {
                my @actual_content_sorted =
                  sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $actual_output_file_name, $columns_to_exclude ) ) );
                my @expected_content_sorted =
                  sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $expected_output_file_name, $columns_to_exclude ) ) );
                is_deeply( \@actual_content_sorted, \@expected_content_sorted,
                    'Actual and expected match output excluding variable columns' );
            }
            else {
                compare_groups_files( $actual_output_file_name, $expected_output_file_name,
                    "Actual and expected sorted output match for '$script_parameters'" );
            }
            unlink($actual_output_file_name);
        }
        close STDOUT;
        close STDERR;
    }

    # Restore stdout.
    open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
    open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";

    # Avoid leaks by closing the independent copies.
    close OLDOUT or die "Can't close OLDOUT: $!";
    close OLDERR or die "Can't close OLDERR: $!";
    unlink('empty_file');
}

sub mock_execute_script_and_check_output_sorted {
    my ( $script_name, $scripts_and_expected_files, $columns_to_exclude ) = @_;

    system('touch empty_file');

    open OLDOUT, '>&STDOUT';
    open OLDERR, '>&STDERR';
    eval("use $script_name ;");
    my $returned_values = 0;
    {
        local *STDOUT;
        open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
        local *STDERR;
        open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";

        for my $script_parameters ( sort keys %$scripts_and_expected_files ) {
            my $full_script = $script_parameters;
            my @input_args = split( " ", $full_script );

            my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
            eval($cmd);
            warn $@ if $@;

            my $actual_output_file_name = $scripts_and_expected_files->{$script_parameters}->[0];

            my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
            ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name  $script_parameters" );
            if ( defined($columns_to_exclude) ) {
                my @actual_content_sorted =
                  sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $actual_output_file_name, $columns_to_exclude ) ) );
                my @expected_content_sorted =
                  sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $expected_output_file_name, $columns_to_exclude ) ) );
                is_deeply( \@actual_content_sorted, \@expected_content_sorted,
                    'Actual and expected match output excluding variable columns' );
            }
            else {
                compare_groups_files( $actual_output_file_name, $expected_output_file_name,
                    "Actual and expected sorted output match for '$script_parameters'" );
            }
            unlink($actual_output_file_name);
        }
        close STDOUT;
        close STDERR;
    }

    # Restore stdout.
    open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
    open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";

    # Avoid leaks by closing the independent copies.
    close OLDOUT or die "Can't close OLDOUT: $!";
    close OLDERR or die "Can't close OLDERR: $!";
    unlink('empty_file');
}

sub compare_tab_files_with_variable_coordinates {
    my ( $actual_file, $expected_file ) = @_;
    ok( -e $actual_file, 'File exists' . $actual_file );

    is(
        _filter_coordinates_from_string($actual_file),
        _filter_coordinates_from_string($expected_file),
        'file contents the same for ' . $actual_file
    );
}

sub _filter_coordinates_from_string {
    my ($file_name) = @_;
    my $file_contents = read_text($file_name);
    my @lines = split( /\n/, $file_contents );
    my $modified_file_contents = '';
    for my $line ( sort @lines ) {
        next if ( $line =~ /(variation|misc_feature|feature)/ );
        $line =~ s!group_[\d]+!group_XX!gi;
        $modified_file_contents .= $line . "\n";
    }
    return $modified_file_contents;
}

sub _exclude_variable_columns_from_spreadsheet {
    my ( $file_name, $columns_to_exclude ) = @_;
    my $file_contents          = read_text($file_name);
    my @lines                  = split( /\n/, $file_contents );
    my $modified_file_contents = '';

    for ( my $i = 0 ; $i < @lines ; $i++ ) {
        my @cells = split( /,/, $lines[$i] );

        for my $col_number ( @{$columns_to_exclude} ) {
            next unless ( defined( $cells[$col_number] ) );
            $cells[$col_number] = '';
        }
        $modified_file_contents .= join( ',', @cells ) . "\n";
    }

    return $modified_file_contents;
}

no Moose;
1;