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1 #! perl
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2 use diagnostics;
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3 use warnings;
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4 no warnings qw/void/;
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5 use strict;
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6 no strict "refs" ;
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7 use Test::More qw( no_plan );
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8 #use Test::More tests => 8 ; ## with MAPPER SEQUENCE
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9 use FindBin ;
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10 use Carp ;
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11
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12 ## Specific Modules
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13 use lib $FindBin::Bin.'/lib' ;
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14 my $binPath = $FindBin::Bin ;
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15 use utilsTest qw( :ALL ) ;
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16 use hmdb_apiTest qw( :ALL ) ;
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17
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18
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19 ## If needed to launch parallele test sequences : SEQ01, SEQ02, SEQ03, ...
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20 my $sequence = 'SEQ02' ;
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21 my $current_test = 1 ;
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22
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23 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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24
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25 ## START of SEQ01 SEQUENCE ##
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26
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27 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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28
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29 if ($sequence eq "SEQ01") {
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30
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31 print "\n\t\t\t\t * * * * * * \n" ;
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32 print "\t * * * - - - Test module utils - - - * * * \n\n" ;
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33
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34 ## - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - - -
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35 # ARGVTS : $argt1, ...
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36 sleep 1 ; print "\n** Test $current_test getHttpFileVersion with a valid url **\n" ; $current_test++ ;
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37 is_deeply( getHttpFileVersionTest ( ## input parameters : here only one argt
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38 'http://www.hmdb.ca/system/downloads/current/urine_metabolites.zip',
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39 ),
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40 'v2018Jul09',
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41 'Method \'getHttpFileVersion\' works with a valid url and return the attended output');
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42
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43
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44 ## - - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - -
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45 # ARGVTS : $argt1, ...
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46 sleep 1 ; print "\n** Test $current_test getHttpFile with a valid url and fileName **\n" ; $current_test++ ;
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47 is_deeply( getHttpFileTest ( ## input parameters : here only one argt
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48 'http://www.hmdb.ca/system/downloads/current/csf_metabolites.zip',
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49 '/tmp/CSF_v2018Jul09/CSF_v2018Jul09.zip'
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50 ),
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51 1,
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52 'Method \'getHttpFile\' works with a valid url and a file name and return the attended output (a file)');
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53
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54
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55 ## - - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - -
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56 # ARGVTS : $argt1, ...
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57 sleep 1 ; print "\n** Test $current_test unzipFile with a valid url, a dir and fileName **\n" ; $current_test++ ;
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58 is_deeply( unzipFileTest ( ## input parameters : here only one argt
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59 '/tmp/CSF_v2018Jul09/CSF_v2018Jul09.zip',
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60 '/tmp/CSF_v2018Jul09/csf_metabolites.xml',
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61 'csf_metabolites.xml'
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62
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63 ),
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64 1,
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65 'Method \'unzipFile\' works with a valid url and a file name and return the attended output (1)');
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66
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67 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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68
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69 ## END of SEQ01 SEQUENCE ##
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70
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71 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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72
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73 }
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74
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75 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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76
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77 ## START of SEQ02 SEQUENCE ##
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78
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79 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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80 elsif ($sequence eq "SEQ02") {
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81 print "\n\t\t\t\t * * * * * * \n" ;
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82 print "\t * * * - - - Test SEQ02 Main script - - - * * * \n\n" ;
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83
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84 ## - - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - -
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85 # ARGVTS : $argt1, ...
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86 # sleep 1 ; print "\n** Test $current_test getMetaboliteFeatures with a valid xml file **\n" ; $current_test++ ;
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87 # is_deeply( getMetaboliteFeaturesTest ( ## input parameters : here only one argt
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88 # '/Users/fgiacomoni/Inra/labs/perl/downloader-bank-hmdb/banks/CSF_v2018Jul09/csf_metabolites.xml',
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89 # ),
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90 # 450,
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91 # 'Method \'getMetaboliteFeatures\' works with a valid xml and return the attended output (HASH)');
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92
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93 ## - - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - -
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94 # ARGVTS : $argt1, ...
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95 sleep 1 ; print "\n** Test $current_test buildMetabolitesArray with a hash of metabolites **\n" ; $current_test++ ;
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96 is_deeply( buildMetabolitesArrayTest ( ## input parameters : here only one argt
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97 { 'HMDB0001565' => { 'metabolite_name' => 'Phosphorylcholine',
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98 'monisotopic_molecular_weight' => '184.073869485',
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99 '[M+H]+' => '185.081145885',
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100 '[M-H]-' => '183.066593085',
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101 'chemical_formula' => 'C5H15NO4P',
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102 'inchikey' => 'YHHSONZFOIEMCP-UHFFFAOYSA-O' },
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103 'HMDB0006088' => { 'monisotopic_molecular_weight' => '180.063388116',
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104 '[M+H]+' => '181.070664516',
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105 '[M-H]-' => '179.056111716',
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106 'inchikey' => 'CDAISMWEOUEBRE-CDRYSYESSA-N',
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107 'chemical_formula' => 'C6H12O6',
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108 'metabolite_name' => 'scyllo-Inositol' }
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109 },
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110 ['HMDB_ID','MzBank', '[M+H]+', '[M-H]-','MetName', 'ChemFormula', 'INChIkey']
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111 ),
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112 [
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113 [
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114 'HMDB_ID',
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115 'MzBank',
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116 '[M+H]+',
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117 '[M-H]-',
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118 'MetName',
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119 'ChemFormula',
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120 'INChIkey'
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121 ],
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122 [
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123 'HMDB0001565',
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124 '184.073869485',
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125 '185.081145885',
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126 '183.066593085',
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127 'Phosphorylcholine',
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128 'C5H15NO4P',
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129 'YHHSONZFOIEMCP-UHFFFAOYSA-O'
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130 ],
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131 [
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132 'HMDB0006088',
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133 '180.063388116',
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134 '181.070664516',
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135 '179.056111716',
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136 'scyllo-Inositol',
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137 'C6H12O6',
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138 'CDAISMWEOUEBRE-CDRYSYESSA-N'
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139 ]
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140 ],
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141 'Method \'buildMetabolitesArray\' works with a valid metabolites list and return the attended output (Array)');
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142
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143 ## - - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - -
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144 # ARGVTS : $argt1, ...
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145 sleep 1 ; print "\n** Test $current_test setMetaboliteAcurrateMzToModesMz with a hash of metabolites **\n" ; $current_test++ ;
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146 is_deeply( setMetaboliteAcurrateMzToModesMzTest ( ## input parameters : here only one argt
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147 'CARD',
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148 [
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149 {
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150 'COMMON_NAME' => 'SM(d18:0/24:1(15Z)(OH))',
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151 'LOCATION' => 'Rumen',
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152 'MZ_AVERAGE' => '829.224',
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153 'INCHI' => 'InChI=1/C47H93N2O7P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-27-28-30-32-34-36-38-44(50)42-47(52)48-45(43-56-57(53,54)55-41-40-49(3,4)5)46(51)39-37-35-33-31-29-26-19-17-15-13-11-9-7-2/h20-21,37,39,44-46,50-51H,6-19,22-36,38,40-43H2,1-5H3,(H-,48,52,53,54)/b21-20-,39-37+/t44?,45-,46+/m0/s1',
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154 'FORMULA' => 'C47H93N2O7P',
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155 'TAXONOMY' => 'Lipids',
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156 'HMDB_ID' => 'HMDB13469',
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157 'KEGG_ID' => 'C00550',
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158 'BIOCYC_ID' => 'Not Available',
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159 'IUPAC' => 'Not Available',
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160 'CAS' => 'Not Available',
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161 'MZ_MONO' => '828.672058'
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162 }
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163 ]
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164 ),
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165 [
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166 {
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167 'MZ_[M-H]-' => '827.6647816',
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168 'COMMON_NAME' => 'SM(d18:0/24:1(15Z)(OH))',
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169 'LOCATION' => 'Rumen',
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170 'MZ_[M+H]+' => '829.6793344',
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171 'MZ_AVERAGE' => '829.224',
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172 'INCHI' => 'InChI=1/C47H93N2O7P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-27-28-30-32-34-36-38-44(50)42-47(52)48-45(43-56-57(53,54)55-41-40-49(3,4)5)46(51)39-37-35-33-31-29-26-19-17-15-13-11-9-7-2/h20-21,37,39,44-46,50-51H,6-19,22-36,38,40-43H2,1-5H3,(H-,48,52,53,54)/b21-20-,39-37+/t44?,45-,46+/m0/s1',
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173 'FORMULA' => 'C47H93N2O7P',
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174 'TAXONOMY' => 'Lipids',
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175 'HMDB_ID' => 'HMDB13469',
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176 'KEGG_ID' => 'C00550',
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177 'BIOCYC_ID' => 'Not Available',
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178 'IUPAC' => 'Not Available',
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179 'CAS' => 'Not Available',
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180 'MZ_MONO' => '828.672058'
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181 }
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182 ],
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183 'Method \'setMetaboliteAcurrateMzToModesMz\' works with XML FORMAT AND a valid metabolites list and return the attended output (Array)');
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184
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185 ## - - - - - - - - - - - - - - - - - - - NEXT - - - - - - - - - - - - - - - - - - -
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186 # ARGVTS : $argt1, ...
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187 sleep 1 ; print "\n** Test $current_test setMetaboliteAcurrateMzToModesMz with a hash of metabolites **\n" ; $current_test++ ;
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188 is_deeply( setMetaboliteAcurrateMzToModesMzTest ( ## input parameters : here only one argt
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189 'XML',
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190 { 'HMDB0001565' => { 'metabolite_name' => 'Phosphorylcholine',
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191 'monisotopic_molecular_weight' => '184.073869485',
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192 'chemical_formula' => 'C5H15NO4P',
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193 'inchikey' => 'YHHSONZFOIEMCP-UHFFFAOYSA-O' },
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194 'HMDB0006088' => { 'monisotopic_molecular_weight' => '180.063388116',
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195 'inchikey' => 'CDAISMWEOUEBRE-CDRYSYESSA-N',
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196 'chemical_formula' => 'C6H12O6',
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197 'metabolite_name' => 'scyllo-Inositol' }
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198 }
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199 ),
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200 { 'HMDB0001565' => { 'metabolite_name' => 'Phosphorylcholine',
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201 'monisotopic_molecular_weight' => '184.073869485',
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202 '[M+H]+' => '185.081145885',
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203 '[M-H]-' => '183.066593085',
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204 'chemical_formula' => 'C5H15NO4P',
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205 'inchikey' => 'YHHSONZFOIEMCP-UHFFFAOYSA-O' },
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206 'HMDB0006088' => { 'monisotopic_molecular_weight' => '180.063388116',
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207 '[M+H]+' => '181.070664516',
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208 '[M-H]-' => '179.056111716',
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209 'inchikey' => 'CDAISMWEOUEBRE-CDRYSYESSA-N',
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210 'chemical_formula' => 'C6H12O6',
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211 'metabolite_name' => 'scyllo-Inositol' }
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212 },
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213 'Method \'setMetaboliteAcurrateMzToModesMz\' works with XML FORMAT AND a valid metabolites list and return the attended output (Array)');
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214
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215 } ## END ELSIF SEQ02
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216
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217 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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218
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219 ## END of SEQ02 SEQUENCE ##
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220
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221 #### #### ##### ###### ################################################ ###### ##### ##### ###### ######
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222
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223
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224 else {
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225 croak "Can\'t launch any test : no sequence clearly defined !!!!\n" ;
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226 }
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227
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