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annotate lib/golm_ws_api.pm @ 3:28d579fa1718 draft default tip

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Master branch Updating - - Fxx
author fgiacomoni
date Wed, 03 Oct 2018 05:35:16 -0400
parents 11779b6402bc
children
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1 package lib::golm_ws_api ;
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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 Data::Dumper ;
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9 #use SOAP::Lite +trace => [qw (debug)];
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10 use SOAP::Lite ;
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11 use JSON ;
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12
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13 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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14
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15 our $VERSION = "1.0";
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16 our @ISA = qw(Exporter);
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17 our @EXPORT = qw( connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results);
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18 our %EXPORT_TAGS = ( ALL => [qw( connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results)] );
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19
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20 =head1 NAME
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21
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22 My::Module - An example module
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23
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24 =head1 SYNOPSIS
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25
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26 use My::Module;
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27 my $object = My::Module->new();
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28 print $object->as_string;
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29
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30 =head1 DESCRIPTION
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31
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32 This module does not really exist, it
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33 was made for the sole purpose of
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34 demonstrating how POD works.
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35
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36 =head1 METHODS
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37
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38 Methods are :
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39
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40 =head2 METHOD new
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41
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42 ## Description : new
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43 ## Input : $self
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44 ## Ouput : bless $self ;
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45 ## Usage : new() ;
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46
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47 =cut
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48
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49 sub new {
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50 ## Variables
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51 my $self={};
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52 bless($self) ;
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53 return $self ;
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54 }
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55 ### END of SUB
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56
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57 =head2 METHOD connectWSlibrarySearchGolm
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58
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59 ## Description : create a soap object throught the webservice LibrarySearch of Golm.
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60 ## Input : $ws_url, $ws_proxy
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61 ## Ouput : $soap ;
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62 ## Usage : my $soap = connectWSlibrarySearchGolm($ws_url, $ws_proxy) ;
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63
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64 =cut
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65
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66 sub connectWSlibrarySearchGolm() {
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67 ## Retrieve Values
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68 my $self = shift ;
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69 my ($ws_url, $ws_proxy) = @_ ;
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70
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71 my $osoap = SOAP::Lite
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72 -> soapversion('1.2')
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73 -> envprefix('soap12')
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74 -> readable(1)
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75 -> uri( $ws_url )
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76 -> proxy( $ws_proxy."/" )
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77 -> on_fault(sub { my($soap, $res) = @_;
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78 eval { die ref $res ? $res->faultstring : $soap->transport->status, "\n"};
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79 return ref $res ? $res : new SOAP::SOM ;
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80 });
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81
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82 return ($osoap);
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83 }
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84 ### END of SUB
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85
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86
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87
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88
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89
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90 =head2 METHOD test_query_golm
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91
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92 ## Description : send a test request (default given on ws website) to golm database.
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93 ## Input : $ws_url, $ws_proxy
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94 ## Ouput : $soap ;
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95 ## Usage : my $soap = test_query_golm($ws_url, $ws_proxy) ;
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96
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97 =cut
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98
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99 sub test_query_golm() {
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100 ## Retrieve Values
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101 my $self = shift ;
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102 my ($ws_url, $ws_proxy) = @_ ;
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103
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104 my $soap = SOAP::Lite
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105 -> uri($ws_url)
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106 -> on_action( sub { join '/', $ws_proxy, $_[1] } )
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107 -> proxy($ws_proxy, timeout => 500);
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108
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109 # Setting Content-Type myself
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110 my $http_request = $soap
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111 ->{'_transport'}
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112 ->{'_proxy'}
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113 ->{'_http_request'};
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114 $http_request->content_type("text/xml; charset=utf-8");
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115
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116 my $method = SOAP::Data->name('LibrarySearch')
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117 ->attr({xmlns => $ws_proxy."/"});
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118
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119 my @params = (
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120 SOAP::Data->name('ri' => 1898),
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121 SOAP::Data->name('riWindow' => 5),
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122 SOAP::Data->name('AlkaneRetentionIndexGcColumnComposition' => 'VAR5'),
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123 SOAP::Data->name('spectrum' => "70 3 71 3 72 16 73 999 74 87 75 78 76 4 77 5 81 1 82 6 83 13 84 4 85 3 86 4 87 5 88 4 89 52 90 4 91 2 97 2 98 1 99 4 100 12 101 16 102 9 103 116 104 11 105 26 106 2 107 1 111 1 112 1 113 4 114 11 115 7 116 5 117 93 118 9 119 8 126 1 127 3 128 3 129 101 130 19 131 25 132 4 133 60 134 8 135 4 140 1 141 1 142 4 143 13 144 2 145 6 146 1 147 276 148 44 149 27 150 3 151 1 156 1 157 70 158 12 159 5 160 148 161 26 162 7 163 8 164 1 168 1 169 2 170 1 172 3 173 4 174 1 175 4 177 4 186 2 187 1 189 28 190 7 191 13 192 2 193 1 201 5 202 1 203 3 204 23 205 162 206 31 207 16 208 2 210 2 214 1 215 2 216 8 217 88 218 18 219 8 220 1 221 6 222 1 229 23 230 6 231 11 232 3 233 4 234 3 235 1 243 1 244 2 245 1 246 2 247 1 256 1 262 3 263 1 269 2 270 1 274 4 275 1 277 4 278 1 291 7 292 2 293 1 300 1 305 4 306 1 307 4 308 1 318 1 319 122 320 37 321 17 322 3 323 1 343 1 364 2 365 1" ) );
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124
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125 my $som = $soap->call($method => @params);
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126 die $som->faultstring if ($som->fault);
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127
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128 ## Get the hits + status of the query
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129 my $results = $som->result->{Results} ;
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130 my $status = $som->result->{Status} ;
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131
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132 if ($status eq 'success' && $results ne '') {
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133 print "\n\n\nThe test request succeeded - Golm Service available.\n\n\n" ;
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134 return 1 ;
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135 }
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136 else { croak "\n\n\nSomething went wrong with the test request. Status delivered by Golm = ".$status."\n\n" ; }
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137 }
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138 ### END of SUB
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139
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140
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141
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142 =head2 METHOD LibrarySearch
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143
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144 ## Description : Matches a single user submitted GC-EI mass spectrum against the Golm Metabolome Database (GMD).
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145 ##  A limited amount of hits can be kept according to the maxHits value and after them being filtered by $filter value
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146 ## Input : $osoap, $ri, $riWindow, $gcColumn, $spectrum, $maxHits
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147 ## Ouput : \@limited_hits, \@json_res
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148 ## Usage : ($limited_hits,$json_res) = LibrarySearch($osoap, $ri, $riWindow, $gcColumn, $spectrum, $maxHits) ;
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149
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150 =cut
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151
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152 sub LibrarySearch() {
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153 ## Retrieve Values
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154 my $self = shift ;
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155 my ($ri, $riWindow, $gcColumn, $spectrum, $maxHits,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,$DotproductDistanceThreshold,
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156 $HammingDistanceThreshold,$EuclideanDistanceThreshold, $ws_url, $ws_proxy, $default_ri, $default_ri_window, $default_gc_column) = @_ ;
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157
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158 #init in case :
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159 $ri = $default_ri if ( !defined $ri ) ;
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160 $riWindow = $default_ri_window if ( !defined $riWindow ) ;
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161 $gcColumn = $default_gc_column if ( !defined $gcColumn ) ;
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162
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163
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164 my $result ;
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165 my @filtered_limited_res = () ;
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166 my @json_res ;
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167
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168 if ( defined $spectrum ){
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169
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170 if ( $spectrum ne '' ) {
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171
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172 my $soap = SOAP::Lite
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173 -> uri($ws_url)
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174 -> on_action( sub { join '/', $ws_proxy, $_[1] } )
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175 -> proxy($ws_proxy);
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176
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177 # Setting Content-Type myself
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178 my $http_request = $soap
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179 ->{'_transport'}
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180 ->{'_proxy'}
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181 ->{'_http_request'};
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182 $http_request->content_type("text/xml; charset=utf-8");
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183
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184 my $method = SOAP::Data->name('LibrarySearch')
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185 ->attr({xmlns => $ws_proxy."/"});
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186
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187 my @params = (
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188 SOAP::Data->name('ri' => $ri),
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189 SOAP::Data->name('riWindow' => $riWindow),
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190 SOAP::Data->name('AlkaneRetentionIndexGcColumnComposition' => $gcColumn),
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191 SOAP::Data->name('spectrum' => $spectrum) ) ;
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192
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193 my $som = $soap->call($method => @params);
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194 die $som->faultstring if ($som->fault);
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195
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196 ## Get the hits + status of the query
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197 my $results = $som->result->{Results} ;
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198 my $status = $som->result->{Status} ;
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199
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200 ## Limitate number of hits returned according to user's $maxHit
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201 ## and filter hits on specific values with thresholds
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202 my @results = @$results ;
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203
0
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204 ### Return all hits
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205 my $oapi = lib::golm_ws_api->new() ;
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206 if ($maxHits == 100 && $status eq 'success') {
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207
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208 my $filtered_res = $oapi->filter_scores_golm_results(\@results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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209 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
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210
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211 if(!@$filtered_res){ push (@$filtered_res , "no results") ; }
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212
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213 return ($filtered_res) ;
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214 }
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215 elsif ($maxHits < 100 && $maxHits > 0 && $status eq 'success'){
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216
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217 my $filtered_res_before_hits_limited = $oapi->filter_scores_golm_results(\@results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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218 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
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219 if (@$filtered_res_before_hits_limited) {
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220
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221 for (my $i=0 ; $i<$maxHits ; $i++) {
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222
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223 push (@filtered_limited_res , @$filtered_res_before_hits_limited[$i]) ;
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224 }
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225 }
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226 else {
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227
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228 if(!@$filtered_res_before_hits_limited){ push (@filtered_limited_res , "no results") ; }
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229 }
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230 return (\@filtered_limited_res) ;
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231 }
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232 else { carp "No match returned from Golm for the query.\n" }
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233 }
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234 else { carp "The spectrum for query is empty, Golm soap will stop.\n" ; }
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235 }
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236 else { carp "The spectrum for query is undef, Golm soap will stop.\n" ; }
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237
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238 # return \@filtered_limited_res ;
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239 }
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240 ### END of SUB
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241
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242
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243
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244
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245 =head2 METHOD filter_scores_golm_results
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246 ## Description : filter golm's hits by distance scores
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247 ## Input : $results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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248 ## $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold
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249 ## Ouput : \@filtered_res ;
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250 ## Usage : my ($filtered_res) = filter_scores_golm_results($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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251 ## $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
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252
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253 =cut
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254
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255 sub filter_scores_golm_results() {
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256 ## Retrieve Values
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257 my $self = shift ;
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258 my ($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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259 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) = @_ ;
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260
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261 my @results = @$results ;
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262 my @filtered_res = () ;
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263
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264 ## Adjust threshold
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265 $JaccardDistanceThreshold = sprintf("%.6f", $JaccardDistanceThreshold) ;
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266 $s12GowerLegendreDistanceThreshold = sprintf("%.6f", $s12GowerLegendreDistanceThreshold) ;
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267 $DotproductDistanceThreshold = sprintf("%.6f", $DotproductDistanceThreshold) ;
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268 # $HammingDistanceThreshold = sprintf("%.6f", $HammingDistanceThreshold);
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269 $EuclideanDistanceThreshold = sprintf("%.6f", $EuclideanDistanceThreshold);
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270
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271 foreach my $res (@results){
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272
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273 $res->{'JaccardDistance'} = sprintf("%.6f", $res->{'JaccardDistance'}) ;
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274 $res->{'s12GowerLegendreDistance'} = sprintf("%.6f", $res->{'s12GowerLegendreDistance'}) ;
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275 $res->{'DotproductDistance'} = sprintf("%.6f", $res->{'DotproductDistance'}) ;
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276 # $res->{'HammingDistance'} = sprintf("%.6f", $res->{'HammingDistance'}) ;
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277 $res->{'EuclideanDistance'} = sprintf("%.6f", $res->{'EuclideanDistance'}) ;
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278
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279 if ($res->{'JaccardDistance'} <= $JaccardDistanceThreshold && $res->{'s12GowerLegendreDistance'} <= $s12GowerLegendreDistanceThreshold
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280 && $res->{'DotproductDistance'} <= $DotproductDistanceThreshold && $res->{'HammingDistance'} <= $HammingDistanceThreshold &&
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281 $res->{'EuclideanDistance'} <= $EuclideanDistanceThreshold) {
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282
0
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283 push (@filtered_res , $res) ;
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284 }
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285 }
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286
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287 my $oapi = lib::golm_ws_api->new() ;
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288 my $sorted_analytes = $oapi->filter_replica_results(\@filtered_res) ;
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289
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290 return $sorted_analytes ;
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291 }
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292
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293
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294
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295 =head2 METHOD _filter_replica_results
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296 ## Description : remove replicated hits, keep the ones with the lowest dot product distance
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297 ## Input : $results
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298 ## Ouput : \@clean_res ;
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299 ## Usage : my ($clean_res) = filter_replica_results($results) ;
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300
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301 =cut
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302
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303 sub filter_replica_results() {
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304 ## Retrieve Values
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305 my $self = shift ;
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306 my ($results) = @_ ;
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307 my %seen ;
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308 my @sortAnalytes = grep { !$seen{$_->{'analyteName'}}++ } sort { $a->{'DotproductDistance'} <=> $b->{'DotproductDistance'} } @$results ;
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309
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310 return \@sortAnalytes ;
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311 }
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312
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313
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314
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315
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316
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317 1 ;
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318
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319
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320 __END__
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321
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322 =head1 SUPPORT
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323
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324 You can find documentation for this module with the perldoc command.
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325
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326 perldoc golm_ws_api.pm
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327
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328 =head1 Exports
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329
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330 =over 4
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331
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332 =item :ALL is connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results
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333
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334 =back
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335
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336 =head1 AUTHOR
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337
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338 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
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339 Gabriel Cretin E<lt>gabriel.cretin@clermont.inra.frE<gt>
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340
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341 =head1 LICENSE
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342
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343 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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344
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345 =head1 VERSION
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346
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347 version 1 : 03 / 06 / 2016
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348
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349 version 2 : 24 / 06 / 2016
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350
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351 =cut