Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate t/hmdb_managerTest.pl @ 7:ecf8e43aceda draft

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planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392
author fgiacomoni
date Fri, 19 Jan 2018 10:27:38 -0500
parents 6091a80df951
children c32280662103
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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::Exception;
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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 ;
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14 my $binPath = $FindBin::Bin ;
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15 use lib::hmdbTest qw( :ALL ) ;
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16
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17
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18 ## To launch the right sequence : API, MAPPER, THREADER, ...
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19 #my $sequence = 'MAPPER' ;
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20 my $sequence = 'MAIN' ;
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21 my $current_test = 1 ;
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22
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23 if ($sequence eq "MAIN") {
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24 print "\n\t\t\t\t * * * * * * \n" ;
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25 print "\t * * * - - - Test HMDB Main script - - - * * * \n\n" ;
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26
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28 print "\n** Test $current_test extract_sub_mz_lists with an empty list of mzs **\n" ; $current_test++;
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29
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30 throws_ok{ extract_sub_mz_listsTest([], 3)} '/The provided mzs list is empty/', 'Method \'extract_sub_mz_lists\' detects empty argument and died correctly' ;
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31
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32 print "\n** Test $current_test extract_sub_mz_lists with a list of mzs and a limit of 3 **\n" ; $current_test++;
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33 is_deeply( extract_sub_mz_listsTest(
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34 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ], 3),
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35 [ [ '175.01', '238.19', '420.16' ], [ '780.32', '956.25', '1100.45' ] ],
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36 'Method \'extract_sub_mz_lists\' works with a list and return a well formated list of sublist of mzs');
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37
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38 print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++;
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39 throws_ok{ prepare_multi_masses_queryTest([])} '/The input method parameter mass list is empty/', 'Method \'prepare_multi_masses_query\' detects empty argument and died correctly' ;
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40
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41 print "\n** Test $current_test prepare_multi_masses_query with a list of mzs **\n" ; $current_test++;
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42 is_deeply( prepare_multi_masses_queryTest(
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43 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ),
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44 '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A',
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45 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying');
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46
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47 print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++;
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48 is_deeply( get_matches_from_hmdb_uaTest(
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49 '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'),
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50 [
4
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51 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
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52 # '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
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53 # '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
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54 # '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
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55 # '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
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56 # '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
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57 # '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
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58 # '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
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59 ## Update format - 2018-01-19... HMDB V04
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60 '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
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61 '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
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62 '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
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63 '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
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64 '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
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65 '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
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66 '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
1
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67 ],
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68 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb');
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69
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70 print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++;
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71 is_deeply (test_matches_from_hmdb_uaTest (),
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72 \'200',
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73 'The HMDB server is available: returns successful HTTP requests' ) ;
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74
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75 print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++;
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76 is_deeply (check_state_from_hmdb_uaTest (\'200'),
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77 1,
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78 'The status 200 returns no error/warn' ) ;
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79
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80 print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++;
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81 throws_ok{ check_state_from_hmdb_uaTest(\'504')}
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82 '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/',
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83 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ;
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84
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85 print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
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86 is_deeply ( parse_hmdb_csv_resultsTest (
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87 [
4
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88 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
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89 # '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
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90 # '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
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91 # '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
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92 # '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
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93 # '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
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94 # '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
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95 # '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
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96 ## Update format - 2018-01-19... HMDB V04
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97 '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
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98 '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
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99 '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
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100 '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
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101 '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
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102 '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
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103 '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
1
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104 ],
4
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105 ['175.01', '238.19', '420.16'],
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106 10
1
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107 ),
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108 [
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109 [
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110 { 'ENTRY_CPD_MZ' => '113.94453531', 'ENTRY_ENTRY_ID' => 'HMDB0060293', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ADDUCT_MZ' => '175.009875', 'ENTRY_DELTA' => '1', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT' => 'M+IsoProp+H' },
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111 {'ENTRY_DELTA' => '4','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+CH3OH+H','ENTRY_CPD_MZ' => '141.975835438','ENTRY_ENTRY_ID' => 'HMDB0003745','ENTRY_FORMULA' => 'C2H6O3S2','ENTRY_ADDUCT_MZ' => '175.009324'},
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112 {'ENTRY_ENTRY_ID' => 'HMDB0031436','ENTRY_CPD_MZ' => '95.987885149','ENTRY_ADDUCT_MZ' => '175.009105','ENTRY_FORMULA' => 'H4O4Si','ENTRY_DELTA' => '5','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+DMSO+H'},
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113 {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0033657','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT' => 'M+H+K','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '5'},
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114 {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0035230','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+H+K','ENTRY_DELTA' => '5'}
1
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115 ],
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116 [],
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117 [
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118 {'ENTRY_FORMULA' => 'C17H17N3O4S','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ENTRY_ID' => 'HMDB0060838','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '2'},
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119 {'ENTRY_DELTA' => '2','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ENTRY_ID' => 'HMDB0060836','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_FORMULA' => 'C17H17N3O4S'}
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120 ]
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121 ],
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122 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;
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123
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124 print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++;
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125 is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ),
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126 [ [], [], [] ],
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127 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ;
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128
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129 print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++;
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130 is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),
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131 [],
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132 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ;
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133 }
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134
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135
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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
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146
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147
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148
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149
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150
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151 ## END of the script