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comparison t/hmdb_managerTest.pl @ 1:6d0a0f8f672a draft

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planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -0500
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children 6091a80df951
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0:9583f9772198 1:6d0a0f8f672a
1 #! perl
2 use diagnostics;
3 use warnings;
4 no warnings qw/void/;
5 use strict;
6 no strict "refs" ;
7 use Test::More qw( no_plan );
8 use Test::Exception;
9 use FindBin ;
10 use Carp ;
11
12 ## Specific Modules
13 use lib $FindBin::Bin ;
14 my $binPath = $FindBin::Bin ;
15 use lib::hmdbTest qw( :ALL ) ;
16
17
18 ## To launch the right sequence : API, MAPPER, THREADER, ...
19 #my $sequence = 'MAPPER' ;
20 my $sequence = 'MAIN' ;
21 my $current_test = 1 ;
22
23 if ($sequence eq "MAIN") {
24 print "\n\t\t\t\t * * * * * * \n" ;
25 print "\t * * * - - - Test HMDB Main script - - - * * * \n\n" ;
26
27
28 print "\n** Test $current_test extract_sub_mz_lists with an empty list of mzs **\n" ; $current_test++;
29
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' ;
31
32 print "\n** Test $current_test extract_sub_mz_lists with a list of mzs and a limit of 3 **\n" ; $current_test++;
33 is_deeply( extract_sub_mz_listsTest(
34 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ], 3),
35 [ [ '175.01', '238.19', '420.16' ], [ '780.32', '956.25', '1100.45' ] ],
36 'Method \'extract_sub_mz_lists\' works with a list and return a well formated list of sublist of mzs');
37
38 print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++;
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' ;
40
41 print "\n** Test $current_test prepare_multi_masses_query with a list of mzs **\n" ; $current_test++;
42 is_deeply( prepare_multi_masses_queryTest(
43 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ),
44 '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A',
45 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying');
46
47 print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++;
48 is_deeply( get_matches_from_hmdb_uaTest(
49 '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'),
50 [
51 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta',
52 '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
53 '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
54 '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
55 '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
56 '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
57 '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
58 '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
59 ],
60 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb');
61
62 print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++;
63 is_deeply (test_matches_from_hmdb_uaTest (),
64 \'200',
65 'The HMDB server is available: returns successful HTTP requests' ) ;
66
67 print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++;
68 is_deeply (check_state_from_hmdb_uaTest (\'200'),
69 1,
70 'The status 200 returns no error/warn' ) ;
71
72 print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++;
73 throws_ok{ check_state_from_hmdb_uaTest(\'504')}
74 '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/',
75 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ;
76
77 print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
78 is_deeply ( parse_hmdb_csv_resultsTest (
79 [
80 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta',
81 '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
82 '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
83 '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
84 '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
85 '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
86 '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
87 '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
88 ],
89 ['175.01', '238.19', '420.16']
90 ),
91 [
92 [
93 { 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_DELTA' => '0.000125', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ENTRY_ID' => 'HMDB60293', 'ENTRY_ADDUCT_MZ' => '175.009875', 'ENTRY_CPD_MZ' => '113.94453531' },
94 { 'ENTRY_ADDUCT' => 'M+CH3OH+H', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000676', 'ENTRY_FORMULA' => 'C2H6O3S2', 'ENTRY_ENTRY_ID' => 'HMDB03745', 'ENTRY_ADDUCT_MZ' => '175.009324', 'ENTRY_CPD_MZ' => '141.975835438' },
95 { 'ENTRY_CPD_MZ' => '95.987885149', 'ENTRY_FORMULA' => 'H4O4Si', 'ENTRY_ENTRY_ID' => 'HMDB31436', 'ENTRY_ADDUCT_MZ' => '175.009105', 'ENTRY_DELTA' => '0.000895', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT' => 'M+DMSO+H' },
96 { 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000914', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_CPD_MZ' => '310.047738052', 'ENTRY_ENTRY_ID' => 'HMDB33657', 'ENTRY_ADDUCT_MZ' => '175.009086', 'ENTRY_FORMULA' => 'C17H10O6' },
97 { 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_DELTA' => '0.000914', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_FORMULA' => 'C17H10O6', 'ENTRY_ADDUCT_MZ' => '175.009086', 'ENTRY_ENTRY_ID' => 'HMDB35230', 'ENTRY_CPD_MZ' => '310.047738052' }
98 ],
99 [],
100 [
101 { 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000683', 'ENTRY_ENTRY_ID' => 'HMDB60838', 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_CPD_MZ' => '359.093976737' },
102 { 'ENTRY_CPD_MZ' => '359.093976737', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_ENTRY_ID' => 'HMDB60836', 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000683', 'ENTRY_ADDUCT' => 'M+IsoProp+H' }
103 ]
104 ],
105 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;
106
107 print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++;
108 is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ),
109 [ [], [], [] ],
110 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ;
111
112 print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++;
113 is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),
114 [],
115 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ;
116 }
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133
134 ## END of the script