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0
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1 package TestHelper;
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2 use Moose::Role;
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3 use Test::Most;
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4 use Data::Dumper;
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5 use File::Slurper qw(read_lines read_text);
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6 use Test::Files;
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7 use Test::Output;
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8
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9 $ENV{PATH} .= ":./bin";
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10
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11 sub compare_files {
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12 my ( $actual_file, $expected_file, $comment ) = @_;
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13 my @actual_lines = sort( read_lines($actual_file) );
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14 my @expected_lines = sort( read_lines($expected_file) );
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15 is_deeply( \@actual_lines, \@expected_lines, $comment );
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16 }
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17
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18 sub compare_groups_files {
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19 my ( $actual_file, $expected_file, $comment ) = @_;
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20 my @actual_lines = sort( read_lines($actual_file) );
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21 my @expected_lines = sort( read_lines($expected_file) );
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22
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23 my @actual_sorted_lines;
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24 for my $line (@actual_lines) {
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25 my @line_details = split( / /, $line );
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26 shift @line_details;
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27 my @sorted = sort(@line_details);
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28 push( @actual_sorted_lines, \@sorted );
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29 }
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30
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31 my @expected_sorted_lines;
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32 for my $line (@expected_lines) {
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33 my @line_details = split( / /, $line );
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34 shift @line_details;
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35 my @sorted = sort(@line_details);
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36 push( @expected_sorted_lines, \@sorted );
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37 }
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38 is_deeply( \@actual_sorted_lines, \@expected_sorted_lines, $comment );
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39 }
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40
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41
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42 sub stdout_should_have
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43 {
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44 my ( $script_name, $parameters, $expected ) = @_;
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45 my @input_args = split( " ", $parameters );
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46 open OLDERR, '>&STDERR';
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47 eval("use $script_name ;");
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48 my $returned_values = 0;
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49 {
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50 local *STDERR;
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51 open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
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52 stdout_like { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
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53 close STDERR;
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54 }
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55 open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
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56 close OLDERR or die "Can't close OLDERR: $!";
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57 }
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58
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59
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60 sub stdout_should_not_have
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61 {
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62 my ( $script_name, $parameters, $expected ) = @_;
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63 my @input_args = split( " ", $parameters );
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64 open OLDERR, '>&STDERR';
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65 eval("use $script_name ;");
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66 my $returned_values = 0;
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67 {
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68 local *STDERR;
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69 open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
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70 stdout_unlike { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
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71 close STDERR;
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72 }
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73 open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
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74 close OLDERR or die "Can't close OLDERR: $!";
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75 }
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76
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77
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78
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79 sub stderr_should_not_have
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80 {
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81 my ( $script_name, $parameters, $expected ) = @_;
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82 my @input_args = split( " ", $parameters );
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83 open OLDOUT, '>&STDOUT';
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84 eval("use $script_name ;");
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85 my $returned_values = 0;
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86 {
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87 local *STDOUT;
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88 open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
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89 stderr_unlike { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
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90 close STDOUT;
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91 }
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92 open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
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93 close OLDOUT or die "Can't close OLDOUT: $!";
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94 }
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95
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96 sub stderr_should_have
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97 {
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98 my ( $script_name, $parameters, $expected ) = @_;
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99 my @input_args = split( " ", $parameters );
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100 open OLDOUT, '>&STDOUT';
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101 eval("use $script_name ;");
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102 my $returned_values = 0;
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103 {
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104 local *STDOUT;
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105 open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
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106 stderr_like { eval("$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;"); } qr/$expected/, "got expected text $expected for $parameters";
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107 close STDOUT;
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108 }
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109 open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
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110 close OLDOUT or die "Can't close OLDOUT: $!";
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111 }
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112
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113
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114 sub mock_execute_script_and_check_output {
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115 my ( $script_name, $scripts_and_expected_files, $columns_to_exclude ) = @_;
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116
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117 system('touch empty_file');
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118
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119 open OLDOUT, '>&STDOUT';
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120 open OLDERR, '>&STDERR';
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121 eval("use $script_name ;");
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122 my $returned_values = 0;
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123 {
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124 local *STDOUT;
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125 open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
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126 local *STDERR;
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127 open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
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128
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129 for my $script_parameters ( sort keys %$scripts_and_expected_files ) {
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130 my $full_script = $script_parameters;
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131 my @input_args = split( " ", $full_script );
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132
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133 my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
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134 eval($cmd);
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135 warn $@ if $@;
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136
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137 my $actual_output_file_name = $scripts_and_expected_files->{$script_parameters}->[0];
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138 my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
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139 ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name $script_parameters" );
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140 if ( defined($columns_to_exclude) ) {
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141 is(
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142 _exclude_variable_columns_from_spreadsheet( $actual_output_file_name, $columns_to_exclude ),
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143 _exclude_variable_columns_from_spreadsheet( $expected_output_file_name, $columns_to_exclude ),
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144 'Actual and expected match output excluding variable columns'
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145 );
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146 }
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147 else {
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148 compare_ok( $actual_output_file_name, $expected_output_file_name,
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149 "Actual and expected output match for '$script_parameters'" );
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150
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151 }
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152 unlink($actual_output_file_name);
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153 }
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154 close STDOUT;
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155 close STDERR;
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156 }
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157
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158 # Restore stdout.
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159 open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
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160 open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
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161
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162 # Avoid leaks by closing the independent copies.
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163 close OLDOUT or die "Can't close OLDOUT: $!";
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164 close OLDERR or die "Can't close OLDERR: $!";
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165 unlink('empty_file');
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166 }
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167
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168 sub mock_execute_script_and_check_output_sorted_groups {
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169 my ( $script_name, $scripts_and_expected_files, $columns_to_exclude ) = @_;
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170
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171 system('touch empty_file');
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172
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173 open OLDOUT, '>&STDOUT';
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174 open OLDERR, '>&STDERR';
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175 eval("use $script_name ;");
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176 my $returned_values = 0;
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177 {
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178 local *STDOUT;
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179 open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
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180 local *STDERR;
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181 open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
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182
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183 for my $script_parameters ( sort keys %$scripts_and_expected_files ) {
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184 my $full_script = $script_parameters;
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185 my @input_args = split( " ", $full_script );
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186
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187 my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
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188 eval($cmd);
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189 warn $@ if $@;
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190
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191 my $actual_output_file_name = $scripts_and_expected_files->{$script_parameters}->[0];
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192
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193 my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
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194 ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name $script_parameters" );
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195 if ( defined($columns_to_exclude) ) {
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196 my @actual_content_sorted =
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197 sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $actual_output_file_name, $columns_to_exclude ) ) );
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198 my @expected_content_sorted =
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199 sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $expected_output_file_name, $columns_to_exclude ) ) );
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200 is_deeply( \@actual_content_sorted, \@expected_content_sorted,
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201 'Actual and expected match output excluding variable columns' );
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202 }
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203 else {
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204 compare_groups_files( $actual_output_file_name, $expected_output_file_name,
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205 "Actual and expected sorted output match for '$script_parameters'" );
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206 }
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207 unlink($actual_output_file_name);
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208 }
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209 close STDOUT;
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210 close STDERR;
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211 }
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212
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213 # Restore stdout.
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214 open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
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215 open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
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216
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217 # Avoid leaks by closing the independent copies.
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218 close OLDOUT or die "Can't close OLDOUT: $!";
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219 close OLDERR or die "Can't close OLDERR: $!";
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220 unlink('empty_file');
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221 }
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222
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223 sub mock_execute_script_and_check_output_sorted {
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224 my ( $script_name, $scripts_and_expected_files, $columns_to_exclude ) = @_;
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225
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226 system('touch empty_file');
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227
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228 open OLDOUT, '>&STDOUT';
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229 open OLDERR, '>&STDERR';
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230 eval("use $script_name ;");
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231 my $returned_values = 0;
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232 {
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233 local *STDOUT;
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234 open STDOUT, '>/dev/null' or warn "Can't open /dev/null: $!";
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235 local *STDERR;
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236 open STDERR, '>/dev/null' or warn "Can't open /dev/null: $!";
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237
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238 for my $script_parameters ( sort keys %$scripts_and_expected_files ) {
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239 my $full_script = $script_parameters;
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240 my @input_args = split( " ", $full_script );
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241
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242 my $cmd = "$script_name->new(args => \\\@input_args, script_name => '$script_name')->run;";
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243 eval($cmd);
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244 warn $@ if $@;
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245
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246 my $actual_output_file_name = $scripts_and_expected_files->{$script_parameters}->[0];
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247
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248 my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
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249 ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name $script_parameters" );
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250 if ( defined($columns_to_exclude) ) {
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251 my @actual_content_sorted =
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252 sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $actual_output_file_name, $columns_to_exclude ) ) );
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253 my @expected_content_sorted =
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254 sort( split( /\n/, _exclude_variable_columns_from_spreadsheet( $expected_output_file_name, $columns_to_exclude ) ) );
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255 is_deeply( \@actual_content_sorted, \@expected_content_sorted,
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256 'Actual and expected match output excluding variable columns' );
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257 }
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258 else {
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259 compare_groups_files( $actual_output_file_name, $expected_output_file_name,
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260 "Actual and expected sorted output match for '$script_parameters'" );
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261 }
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262 unlink($actual_output_file_name);
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263 }
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264 close STDOUT;
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265 close STDERR;
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266 }
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267
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268 # Restore stdout.
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269 open STDOUT, '>&OLDOUT' or die "Can't restore stdout: $!";
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270 open STDERR, '>&OLDERR' or die "Can't restore stderr: $!";
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271
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272 # Avoid leaks by closing the independent copies.
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273 close OLDOUT or die "Can't close OLDOUT: $!";
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274 close OLDERR or die "Can't close OLDERR: $!";
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275 unlink('empty_file');
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276 }
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277
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278 sub compare_tab_files_with_variable_coordinates {
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279 my ( $actual_file, $expected_file ) = @_;
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280 ok( -e $actual_file, 'File exists' . $actual_file );
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281
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282 is(
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283 _filter_coordinates_from_string($actual_file),
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284 _filter_coordinates_from_string($expected_file),
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285 'file contents the same for ' . $actual_file
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286 );
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287 }
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288
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289 sub _filter_coordinates_from_string {
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290 my ($file_name) = @_;
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291 my $file_contents = read_text($file_name);
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292 my @lines = split( /\n/, $file_contents );
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293 my $modified_file_contents = '';
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294 for my $line ( sort @lines ) {
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295 next if ( $line =~ /(variation|misc_feature|feature)/ );
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296 $line =~ s!group_[\d]+!group_XX!gi;
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297 $modified_file_contents .= $line . "\n";
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298 }
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299 return $modified_file_contents;
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300 }
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301
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302 sub _exclude_variable_columns_from_spreadsheet {
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303 my ( $file_name, $columns_to_exclude ) = @_;
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304 my $file_contents = read_text($file_name);
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305 my @lines = split( /\n/, $file_contents );
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306 my $modified_file_contents = '';
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307
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308 for ( my $i = 0 ; $i < @lines ; $i++ ) {
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309 my @cells = split( /,/, $lines[$i] );
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310
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311 for my $col_number ( @{$columns_to_exclude} ) {
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312 next unless ( defined( $cells[$col_number] ) );
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313 $cells[$col_number] = '';
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314 }
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315 $modified_file_contents .= join( ',', @cells ) . "\n";
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316 }
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317
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318 return $modified_file_contents;
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319 }
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320
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321 no Moose;
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322 1;
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323
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