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annotate t/lib/golm_ws_api_test.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 e3d43b8c987b
children
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1 package lib::golm_ws_api_test ;
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2
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3 use diagnostics; # this gives you more debugging information
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4 use warnings; # this warns you of bad practices
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5 use strict; # this prevents silly errors
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6 use Exporter ;
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7 use Carp ;
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8
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9 use Data::Dumper ;
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10
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11 our $VERSION = "1.0";
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12 our @ISA = qw(Exporter);
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13 our @EXPORT = qw( keep_only_max_massesTest keep_only_max_intensitiesTest test_query_golmTest connectWSlibrarySearchGolmTest LibrarySearchTest encode_spectrum_for_queryTest get_mzsTest get_intensitiesTest get_masses_from_stringTest get_intensities_from_stringTest sorting_descending_intensities1Test sorting_descending_intensities2Test remove_redundants1Test remove_redundants2Test filter_scores_golm_resultsTest filter_replica_resultsTest apply_relative_intensityTest);
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14 our %EXPORT_TAGS = ( ALL => [qw( keep_only_max_massesTest keep_only_max_intensitiesTest test_query_golmTest connectWSlibrarySearchGolmTest LibrarySearchTest encode_spectrum_for_queryTest get_mzsTest get_intensitiesTest get_masses_from_stringTest get_intensities_from_stringTest sorting_descending_intensities1Test sorting_descending_intensities2Test remove_redundants1Test remove_redundants2Test filter_scores_golm_resultsTest filter_replica_resultsTest apply_relative_intensityTest)] );
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17 use lib::golm_ws_api qw( :ALL ) ;
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18 use lib::msp qw( :ALL ) ;
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19 use lib::output qw( :ALL ) ;
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20
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21 ### Test API module ###
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22
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23 sub test_query_golmTest {
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24 my ($ws_url, $ws_proxy) = @_;
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25 my $oBih = lib::golm_ws_api->new() ;
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26 my ($status) = $oBih->test_query_golm($ws_url, $ws_proxy) ;
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27 return ($status) ;
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28 }
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30
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31 sub connectWSlibrarySearchGolmTest {
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32 my ($ws_url, $ws_proxy) = @_ ;
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33 my $oBih = lib::golm_ws_api->new() ;
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34 my ($soap) = $oBih->connectWSlibrarySearchGolm($ws_url, $ws_proxy) ;
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35 return ($soap) ;
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36 }
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39 sub LibrarySearchTest {
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40 my ($ri, $riWindow, $gcColumn, $spectrum, $maxHits, $JaccardDistanceThreshold,
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41 $s12GowerLegendreDistanceThreshold,$DotproductDistanceThreshold,$HammingDistanceThreshold,
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42 $EuclideanDistanceThreshold,$ws_url, $ws_proxy,$default_ri, $default_ri_window, $default_gc_column) = @_ ;
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43 my $oBih = lib::golm_ws_api->new() ;
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44 my ($limited_hits) =$oBih->LibrarySearch($ri, $riWindow, $gcColumn, $spectrum, $maxHits, $JaccardDistanceThreshold,
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45 $s12GowerLegendreDistanceThreshold,$DotproductDistanceThreshold,$HammingDistanceThreshold,
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46 $EuclideanDistanceThreshold,$ws_url, $ws_proxy,$default_ri, $default_ri_window, $default_gc_column) ;
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47 return ($limited_hits) ;
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48 }
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50
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51 sub filter_scores_golm_resultsTest {
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52 my ($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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53 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) = @_ ;
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54 my $oBih = lib::golm_ws_api->new() ;
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55 my ($filtered_res_before_hits_limited) = $oBih->filter_scores_golm_results($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
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56 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
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57 return ($filtered_res_before_hits_limited) ;
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58 }
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60
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61 sub filter_replica_resultsTest {
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62 my ($results) = @_ ;
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63 my $oBih = lib::golm_ws_api->new() ;
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64 my ($sortAnalytes) = $oBih->filter_replica_results($results) ;
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65 return ($sortAnalytes) ;
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66 }
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70
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71 ### Test MSP module ###
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72
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73 sub get_mzsTest {
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74 my ($inputSpectra, $mzRes) = @_;
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75 my $omsp = lib::msp->new();
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76 my $mzs = $omsp->get_mzs ($inputSpectra, $mzRes) ;
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77 return($mzs) ;
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78 }
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80
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81 sub get_intensitiesTest {
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82 my ($inputSpectra) = @_;
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83 my $omsp = lib::msp->new();
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84 my $intensities = $omsp->get_intensities($inputSpectra) ;
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85 return($intensities) ;
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86 }
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88
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89 sub get_masses_from_stringTest {
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90 my ($inputSpectra, $mzRes) = @_;
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91 my $omsp = lib::msp->new();
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92 my ($ref_mzs_res) = $omsp->get_masses_from_string($inputSpectra, $mzRes) ;
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93 return($ref_mzs_res) ;
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94 }
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96
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97 sub get_intensities_from_stringTest {
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98 my ($inputSpectra) = @_;
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99 my $omsp = lib::msp->new();
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100 my ($ref_ints_res) = $omsp->get_intensities_from_string($inputSpectra) ;
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101 return($ref_ints_res) ;
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102 }
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103
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104
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105 sub keep_only_max_massesTest {
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106 my ($ref_mzs_res, $maxIons) = @_;
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107 my $omsp = lib::msp->new();
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108 my ($mzs_res_sorted) = $omsp->keep_only_max_masses($ref_mzs_res, $maxIons) ;
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109 return($mzs_res_sorted) ;
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110 }
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111
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112
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113 sub keep_only_max_intensitiesTest {
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114 my ($ref_ints_res, $maxIons) = @_;
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115 my $omsp = lib::msp->new();
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116 my ($ints_res_sorted) = $omsp->keep_only_max_intensities($ref_ints_res, $maxIons) ;
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117 return($ints_res_sorted) ;
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118 }
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119
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120
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121 sub sorting_descending_intensities1Test {
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122 my ($uniq_total_masses, $uniq_total_intensities) = @_;
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123 my $omsp = lib::msp->new();
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124 my ($mzs_res_sorted, $ints_res_sorted) = $omsp->sorting_descending_intensities($uniq_total_masses, $uniq_total_intensities) ;
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125 return($mzs_res_sorted) ;
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126 }
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127
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128
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129 sub sorting_descending_intensities2Test {
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130 my ($uniq_total_masses, $uniq_total_intensities) = @_;
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131 my $omsp = lib::msp->new();
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132 my ($mzs_res_sorted, $ints_res_sorted) = $omsp->sorting_descending_intensities($uniq_total_masses, $uniq_total_intensities) ;
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133 return($ints_res_sorted) ;
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134 }
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135
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136
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137 sub encode_spectrum_for_queryTest {
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138 my ($mzs_res_sorted, $relative_ints_res) = @_;
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139 my $omsp = lib::msp->new();
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140 my $encoded_spectra = $omsp->encode_spectrum_for_query($mzs_res_sorted, $relative_ints_res) ;
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141 return ($encoded_spectra) ;
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142 }
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143
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144
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145 sub remove_redundants1Test {
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146 my ($ref_mzs_res, $ref_ints_res) = @_;
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147 my $omsp = lib::msp->new();
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148 my ($uniq_masses , $uniq_intensities) = $omsp->remove_redundants($ref_mzs_res, $ref_ints_res, $ref_mzs_res, $ref_ints_res) ;
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149 return ($uniq_masses ) ;
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150 }
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151
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152
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153 sub remove_redundants2Test {
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154 my ($ref_mzs_res, $ref_ints_res) = @_;
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155 my $omsp = lib::msp->new();
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156 my ($uniq_masses , $uniq_intensities) = $omsp->remove_redundants($ref_mzs_res, $ref_ints_res, $ref_mzs_res, $ref_ints_res) ;
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157 return ($uniq_intensities) ;
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158 }
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159
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160
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161 sub apply_relative_intensityTest {
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162 my ($uniq_total_intensities) = @_;
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163 my $omsp = lib::msp->new();
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164 my ($relative_ints_res) = $omsp->apply_relative_intensity($uniq_total_intensities) ;
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165 return ($relative_ints_res) ;
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166 }
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167
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168
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169
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170
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171
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172 1 ;