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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/lib/TestHelper.pm	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,323 @@
+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;
+