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Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx
author fgiacomoni
date Thu, 19 May 2022 13:43:09 +0000
parents 625fa968d99a
children
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1
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1 package lib::csv ;
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2
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3 use strict;
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4 use warnings ;
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5 use Exporter ;
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6 use Carp ;
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7
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8 use Text::CSV ;
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10 use Data::Dumper ;
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11
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12 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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13
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14 our $VERSION = "1.0";
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15 our @ISA = qw(Exporter);
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16 our @EXPORT = qw( get_csv_object get_value_from_csv_multi_header );
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17 our %EXPORT_TAGS = ( ALL => [qw( get_csv_object get_value_from_csv_multi_header )] );
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18
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19 =head1 NAME
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20
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21 My::Module - An example module
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22
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23 =head1 SYNOPSIS
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24
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25 use My::Module;
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26 my $object = My::Module->new();
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27 print $object->as_string;
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28
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29 =head1 DESCRIPTION
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30
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31 This module does not really exist, it
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32 was made for the sole purpose of
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33 demonstrating how POD works.
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34
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35 =head1 METHODS
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36
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37 Methods are :
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38
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39 =head2 METHOD new
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40
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41 ## Description : new
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42 ## Input : $self
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43 ## Ouput : bless $self ;
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44 ## Usage : new() ;
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45
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46 =cut
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47
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48 sub new {
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49 ## Variables
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50 my $self={};
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51 bless($self) ;
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52 return $self ;
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53 }
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54 ### END of SUB
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55
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56 =head2 METHOD get_csv_object
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57
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58 ## Description : builds a csv object and etablishes format
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59 ## Input : $separator
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60 ## Output : $csv
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61 ## Usage : my ( $csv ) = get_csv_object( $separator ) ;
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62
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63 =cut
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64 ## START of SUB
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65 sub get_csv_object {
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66 ## Retrieve Values
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67 my $self = shift ;
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68 my ( $separator ) = @_ ;
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69
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70 # my $csv = Text::CSV->new({'sep_char' => "$separator"});
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71 my $csv = Text::CSV->new ( {'sep_char' => "$separator", binary => 1 } ) # should set binary attribute.
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72 or die "Cannot use CSV: ".Text::CSV->error_diag ();
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73
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74 return($csv) ;
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75 }
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76 ## END of SUB
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77
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78 =head2 METHOD get_value_from_csv_multi_header
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79
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80 ## Description : extract a targeted column in a csv file
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81 ## Input : $csv, $file, $column, $is_header, $nb_header
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82 ## Output : $value
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83 ## Usage : my ( $value ) = get_value_from_csv_multi_header( $csv, $file, $column, $is_header, $nb_header ) ;
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84
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85 =cut
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86 ## START of SUB
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87 sub get_value_from_csv_multi_header {
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88 ## Retrieve Values
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89 my $self = shift ;
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90 my ( $csv, $file, $column, $is_header, $nb_header ) = @_ ;
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91
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92 my @value = () ;
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93
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94 ## Adapte the number of the colunm : (nb of column to position in array)
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95 $column = $column - 1 ;
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96
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97 open (CSV, "<", $file) or die $! ;
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98
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99 my $line = 0 ;
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100
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101 while (<CSV>) {
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102 $line++ ;
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103 chomp $_ ;
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104 # file has a header
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105 if ( defined $is_header and $is_header eq 'yes') { if ($line <= $nb_header) { next ; } }
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106 # parsing the targeted column
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107 if ( $csv->parse($_) ) {
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108 my @columns = $csv->fields();
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109 push ( @value, $columns[$column] ) ;
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110 }
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111 else {
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112 my $err = $csv->error_input;
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113 die "Failed to parse line: $err";
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114 }
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115 }
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116 close CSV;
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117 return(\@value) ;
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118 }
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119 ## END of SUB
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120
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121 =head2 METHOD parse_csv_object
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122
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123 ## Description : parse_all csv object and return a array of rows
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124 ## Input : $csv, $file
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125 ## Output : $csv_matrix
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126 ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file ) ;
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127
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128 =cut
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129 ## START of SUB
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130 sub parse_csv_object {
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131 ## Retrieve Values
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132 my $self = shift ;
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133 my ( $csv, $file ) = @_ ;
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134
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135 my @csv_matrix = () ;
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136
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137 open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!";
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138
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139 while ( my $row = $csv->getline( $fh ) ) {
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140 push @csv_matrix, $row;
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141 }
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142 $csv->eof or $csv->error_diag();
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143 close $fh;
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144
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145 return(\@csv_matrix) ;
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146 }
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147 ## END of SUB
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148
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149 =head2 METHOD parse_allcsv_object
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150
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151 ## Description : parse_all csv object and return a array of rows with or without header
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152 ## Input : $csv, $file, $keep_header
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153 ## Output : $csv_matrix
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154 ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file, $keep_header ) ;
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155
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156 =cut
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157 ## START of SUB
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158 sub parse_allcsv_object {
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159 ## Retrieve Values
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160 my $self = shift ;
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161 my ( $csv, $file, $keep_header ) = @_ ;
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162
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163 my @csv_matrix = () ;
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164 my $line = 1 ;
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165
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166 open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!";
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167
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168 while ( my $row = $csv->getline( $fh ) ) {
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169 if ( ( $keep_header eq 'n' ) and ($line == 1) ) { }
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170 else { push @csv_matrix, $row; }
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171 $line ++ ;
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172 }
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173 my $status = $csv->eof or $csv->error_diag();
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174 close $fh;
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175
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176 return(\@csv_matrix, $status) ;
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177 }
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178 ## END of SUB
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179
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180
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181 =head2 METHOD write_csv_from_arrays
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182
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183 ## Description : write a csv file from list of rows
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184 ## Input : $csv, $file_name, $rows
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185 ## Output : $csv_file
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186 ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $rows ) ;
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187
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188 =cut
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189 ## START of SUB
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190 sub write_csv_from_arrays {
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191 ## Retrieve Values
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192 my $self = shift ;
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193 my ( $csv, $file_name, $rows ) = @_ ;
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194
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195 my $fh = undef ;
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196 $csv->eol ("\n"); ## end-of-line string to add to rows
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197 # $csv->quote_char(undef) ;
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198 open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!";
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199
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200 my $status = $csv->print ($fh, $_) for @{$rows};
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201 close $fh or die "$file_name: $!";
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202
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203 return(\$file_name) ;
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204 }
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205 ## END of SUB
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206
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207
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208 =head2 METHOD write_csv_from_hash
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209
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210 ## Description : write a csv file from simple hash with headers
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211 ## Input : $csv, $file_name, $headers, $arrayofhash
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212 ## Output : $csv_file
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213 ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $headers, $arrayofhash ) ;
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214
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215 =cut
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216 ## START of SUB
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217 sub write_csv_from_array_of_hash {
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218 ## Retrieve Values
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219 my $self = shift ;
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220 my ( $csv, $file_name, $headers, $hash ) = @_ ;
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221
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222 my $fh = undef ;
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223 $csv->eol ("\n"); ## end-of-line string to add to rows
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224 $csv->quote_char(undef) ;
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225 open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!";
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226
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227 if (defined $headers) {
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228 for my $field (@$headers) { print $fh join('\t', $field), "\n"; } ;
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229 }
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230
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231 for my $row (keys %{$hash}) {
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232 print $fh join('\t', map { $_, $row->{$_} } sort keys %$row), "\n";
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233 }
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234
1
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235 close $fh or die "$file_name: $!";
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236
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237 return(\$file_name) ;
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238 }
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239 ## END of SUB
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240
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241 1 ;
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242
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243
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244 __END__
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245
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246 =head1 SUPPORT
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247
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248 You can find documentation for this module with the perldoc command.
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249
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250 perldoc csv.pm
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251
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252 =head1 Exports
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253
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254 =over 4
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255
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256 =item :ALL is get_csv_object, get_value_from_csv_multi_header
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257
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258 =back
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259
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260 =head1 AUTHOR
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261
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262 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
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263
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264 =head1 LICENSE
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265
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266 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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267
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268 =head1 VERSION
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269
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270 version 1 : 23 / 10 / 2013
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271
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272 version 2 : ??
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273
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274 =cut