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1 #!/usr/bin/env perl
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2 use strict;
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3 use warnings;
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4
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5 my $progname = shift;
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6 $progname =~ s/\.acd$//g;
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7 my $progfile = "/usr/local/share/EMBOSS/acd/$progname.acd";
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8 open my $acdfh, "<", $progfile;
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9 open my $xmlfh, ">", "$progname.xml";
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10
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11 my $tool;
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12 my $description;
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13 my $command;
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14 my @params;
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15 my @args;
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16 my $help;
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17 my $plot = 0+`grep -c 'toggle: plot' $progfile`;
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18 my $pngout = 0+`grep -c 'string: format' $progfile`;
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19
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20 while(<$acdfh>) {
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21 chomp;
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22 if(/\s*application\s*:\s*\w+\s*\[\s*$/../^\s*\]\s*$/) {
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23 if(/\s*application\s*:\s*(\w+)\s*\[\s*$/) {
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24 $tool = qq(<tool id="EMBOSS: $1" name="$1" version="1.0.2">);
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25 }
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26
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27 if(/\s*documentation:\s*"([^"]+)"?\s*/) {
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28 my $tmp = $1;
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29 if(/\s*documentation:\s*".+"\s*/) {
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30 $description = qq( <description>$tmp</description>);
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31 } else {
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32 while(<$acdfh>) {
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33 if(/\s*(.*)"/) {
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34 $tmp.= " $1";
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35 last;
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36 } elsif(/\s*(.*)\s*/) {
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37 $tmp .= " $1";
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38 }
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39 }
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40 $description = qq( <description>$tmp</description>);
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41 }
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42 }
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43 }
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44
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45 if(/\s*section\s*:\s*advanced\s*\[/../\s*endsection:\s*advanced/) {
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46 if(/\s*section\s*:\s*advanced\s*\[/../\]/ or /\s*endsction:\s*advanced/) {
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47 next;
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48 }
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49
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50 if(/\s*\w+\s*:\s*\w+\s*\[/../\s*\]/) {
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51 if(/\s*(\w+)\s*:\s*(\w+)\s*\[/) {
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52 my ($type, $name) = ($1, $2);
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53 my $information;
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54 my $default;
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55 my @values;
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56
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57 next if $name eq "accid";
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58 next if $name eq "plot";
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59
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60 push @args, $name;
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61
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62 while(<$acdfh>) {
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63 chomp;
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64 if(/\]/) {
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65 last;
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66 }
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67 if(/\s*information:\s*"([^"]+)"?\s*/) {
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68 my $tmp = $1;
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69 if(/\s*information:\s*".+"\s*/) {
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70 $information = $tmp;
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71 } else {
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72 while(<$acdfh>) {
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73 if(/\s*(.*)"/) {
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74 $tmp.= " $1";
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75 last;
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76 } elsif(/\s*(.*)\s*/) {
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77 $tmp .= " $1";
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78 }
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79 }
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80 $information = $tmp;
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81 }
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82 }
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83
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84 if(/\s*default:\s*"(.+)"\s*/) {
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85 $default = $1;
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86 }
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87
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88 if(/\s*values:\s*"(.+)"\s*/) {
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89 @values = split ";", $1;
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90 }
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91 }
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92 #print "$type\t$name\t$information";
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93 #print "\t$default" if defined $default;
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94 #print "\n";
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95 my $param;
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96
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97 if($default) {
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98 $default = "yes" if $default eq "Y";
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99 $default = "no" if $default eq "N";
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100 $default = "[^ACDEFGHIKLMNPQRSTVWYacgtU]" if $name eq "delkey";
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101 } else {
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102 $default = "";
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103 }
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104
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105 if($type eq "boolean") {
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106 $param = <<EOS;
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107 <param name="$name" type="select" value="$default">
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108 <label>$information</label>
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109 <option value="no">No</option>
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110 <option value="yes">Yes</option>
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111 </param>
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112 EOS
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113 }
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114
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115 if($type =~ /(integer)|(float)|(string)/) {
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116 $type =~ s/string/text/g;
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117 $param = <<EOS;
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118 <param name="$name" size="4" type="$type" value="$default">
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119 <label>$information</label>
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120 </param>
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121 EOS
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122 }
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123
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124 if($type =~ /selection/) {
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125 my $vals = join "\n", map{
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126 " <option value=\"$_\">". ucfirst($_) ."</option>"
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127 }@values;
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128 $param = <<EOS
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129 <param name="$name" type="select" value="$default">
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130 <label>$information</label>
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131 $vals
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132 </param>
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133 EOS
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134 }
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135
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136 print "$type: $name\n";
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137 if($param && length $param) {
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138 chomp($param);
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139 push @params, $param;
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140 }
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141 }
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142 }
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143 }
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144 }
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145 close $acdfh;
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146
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147 my $args = join(" ", map{"-$_ \$$_"}@args);
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148
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149 my $paramstr = "";
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150 foreach my $param (@params) {
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151 $paramstr .= "$param\n";
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152 }
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153
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154 my $outputs;
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155
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156 if($plot) {
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157 $command = "<command interpreter=\"perl\">gembassy_calcandplot_wrapper.pl $progname -sequence \$input1 $args -auto \$out_file1 \$out_file2</command>";
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158 $outputs = <<EOS;
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159 <data format="csv" name="out_file1" label="\${tool.name} data for \${input1.name}" />
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160 <data format="png" name="out_file2" label="\${tool.name} plot for \${input1.name}" />
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161 EOS
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162 } elsif($pngout) {
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163 $command = "<command interpreter=\"perl\">emboss_single_outputfile_wrapper.pl $progname -sequence \$input1 -format png -goutfile \$out_file1 -auto $args</command>";
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164 $outputs = <<EOS;
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165 <data format="png" name="out_file1" label="\${tool.name} for \${input1.name}" />
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166 EOS
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167 } else {
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168 $command = "<command>$progname -sequence \$input1 $args -auto -outfile \$out_file1</command>";
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169 printf(STDERR "Enter output data format of $progname (1: txt 2: csv): ");
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170 chomp(my $format = <>);
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171 $format = $format == 1 ? "txt" : "csv";
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172 $outputs = <<EOS;
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173 <data format="$format" name="out_file1" label="\${tool.name} for \${input1.name}" />
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174 EOS
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175 }
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176 chomp $outputs;
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177
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178 print $xmlfh <<EOS;
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179 $tool
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180 $description
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181 $command
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182 <inputs>
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183 <param format="data" name="input1" type="data">
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184 <label>Sequence</label>
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185 </param>
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186 $paramstr
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187 </inputs>
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188 <outputs>
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189 $outputs
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190 </outputs>
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191 </tool>
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192 EOS
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193
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194 close $xmlfh;
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