Mercurial > repos > fgiacomoni > bank_inhouse
comparison t/bih_managerTest.t @ 0:be582bcd6585 draft
Master branch Updating - - Fxx
author | fgiacomoni |
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date | Thu, 04 Oct 2018 10:37:14 -0400 |
parents | |
children | 52798007c6b2 |
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-1:000000000000 | 0:be582bcd6585 |
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1 #! perl | |
2 use diagnostics; | |
3 use warnings; | |
4 no warnings qw/void/; | |
5 use strict; | |
6 no strict "refs" ; | |
7 use Test::More tests => 36 ; | |
8 use FindBin ; | |
9 use Data::Dumper ; | |
10 | |
11 ## Specific Modules | |
12 use lib $FindBin::Bin ; | |
13 my $binPath = $FindBin::Bin ; | |
14 use lib::bihTest qw( :ALL ) ; | |
15 | |
16 ## testing check_interval | |
17 print "\n-- test whether a value is in the interval defines\n\n" ; | |
18 #01 | |
19 is ( check_interval_Test('test', '0', '1'), "'test' isn't a valid number!", 'Works with a value that is not a number'); | |
20 #02 | |
21 is ( check_interval_Test('', '0', '1'), "'' isn't a valid number!", 'Works with a value that is not a number'); | |
22 #03 | |
23 is ( check_interval_Test('-0.5', '-1', '0'), "OK", 'Works with a negative float'); | |
24 #04 | |
25 is ( check_interval_Test('-0.5', '0', '1'), "'-0.5' is below the minimum!", 'Works with a number below the minimum!'); | |
26 #05 | |
27 is ( check_interval_Test('2', '0', '1'), "'2' is greater than the maximum!", 'Works with a number greater than the maximum!'); | |
28 print "\n--\n" ; | |
29 | |
30 ## testing format_manual_masses | |
31 print "\n-- Test format manual list of values lib for values (ex=> masses)\n\n" ; | |
32 #06 | |
33 isa_ok( format_manual_list_values_Testvalues('562.0235', ' '), 'ARRAY' ); | |
34 #07 | |
35 is_deeply(format_manual_list_values_Testvalues('562.0235', ' '), [562.0235], 'Works with \'562.0235\' for mass'); | |
36 #08 | |
37 is_deeply(format_manual_list_values_Testvalues('562.0235 987.4568', ' '), [562.0235, 987.4568], 'Works with \'562.0235 987.4568\' for masses'); | |
38 #09 | |
39 is_deeply(format_manual_list_values_Testvalues('562.0235;987.4568', ';'), [562.0235, 987.4568], 'Works with \'562.0235;987.4568\' for masses'); | |
40 print "\n--\n" ; | |
41 | |
42 print "\n-- Test format manual list of values lib for ids\n\n" ; | |
43 #10 | |
44 isa_ok( format_manual_list_values_Testids('562.0235', ' '), 'ARRAY' ); | |
45 #11 | |
46 is_deeply(format_manual_list_values_Testids('562.0235', ' '), ['value_1'], 'Works with \'562.0235\' for ids'); | |
47 #12 | |
48 is_deeply(format_manual_list_values_Testids('562.0235 987.4568', ' '), ['value_1', 'value_2'], 'Works with \'562.0235 987.4568\' for ids'); | |
49 #13 | |
50 is_deeply(format_manual_list_values_Testids('562.0235 987.4568 ', ' '), ['value_1', 'value_2'], 'Works with \'562.0235 987.4568 \' for ids'); | |
51 #14 | |
52 is_deeply(format_manual_list_values_Testids('562.0235 987.4568 52.0235 98.48 62.0235 987.68 152.05 8.48 562.0235', ' '), ['value_1', 'value_2','value_3', 'value_4','value_5', 'value_6','value_7', 'value_8', 'value_9'], 'Works with 9 masses for ids'); | |
53 #15 | |
54 is_deeply(format_manual_list_values_Testids('562.0235 987.4568 52.0235 98.48 62.0235 987.68 152.05 8.48 562.0235 987.4568', ' '), ['value_01', 'value_02','value_03', 'value_04','value_05', 'value_06','value_07', 'value_08', 'value_09', 'value_10'], 'Works with 10 masses for ids'); | |
55 #16 | |
56 is_deeply(format_manual_list_values_Testids('562.0235 987.4568 52.0235 98.48 62.0235 987.68 152.05 8.48 562.0235 987.4568 52.0235 98.48 62.0235 987.68 152.05 8.48', ' '), ['value_01', 'value_02','value_03', 'value_04','value_05', 'value_06','value_07', 'value_08', 'value_09', 'value_10', 'value_11', 'value_12', 'value_13', 'value_14', 'value_15', 'value_16'], 'Works with 16 masses for ids'); | |
57 print "\n--\n" ; | |
58 | |
59 ## testing manage_mode | |
60 #print "\n-- Test manage_mode lib\n\n" ; | |
61 #09 | |
62 #isa_ok( manage_mode_Testionization('positive,negative,neutral'), 'ARRAY' ); | |
63 #10 | |
64 #is_deeply(manage_mode_Testionization('positive,negative,neutral'), ['positive', 'negative', 'neutral'], 'Works with \'562.0235\' for ids'); | |
65 #14 | |
66 #isa_ok( format_manual_list_values_Testids('562.0235 987.4568'), 'ARRAY' ); | |
67 #15 | |
68 #is_deeply(format_manual_list_values_Testids('562.0235 987.4568'), ['mass_1', 'mass_2'], 'Works with \'562.0235 987.4568\' for ids'); | |
69 #16 | |
70 #is_deeply(format_manual_list_values_Testids('562.0235 987.4568 52.0235 98.48 62.0235 987.68 152.05 8.48 562.0235 987.4568 52.0235 98.48 62.0235 987.68 152.05 8.48'), ['mass_01', 'mass_02','mass_03', 'mass_04','mass_05', 'mass_06','mass_07', 'mass_08', 'mass_09', 'mass_10', 'mass_11', 'mass_12', 'mass_13', 'mass_14', 'mass_15', 'mass_16'], 'Works with 16 masses for ids'); | |
71 #print "\n--\n" ; | |
72 | |
73 ## testing mz_delta_conversion | |
74 print "\n-- Test mz_delta_conversion lib\n\n" ; | |
75 #17 | |
76 is ( mz_delta_conversion_Testmin(100, 'Da', 0.005), 99.995, 'Works with \'100, Da, 0.005\' for minimum'); | |
77 #18 | |
78 is ( mz_delta_conversion_Testmax(100, 'Da', 0.005), 100.0050000001, 'Works with \'100, Da, 0.005\' for maximum'); | |
79 #19 | |
80 is ( mz_delta_conversion_Testmin(500, 'Da', 0.005), 499.995, 'Works with \'500, Da, 0.005\' for minimum'); | |
81 #20 | |
82 is ( mz_delta_conversion_Testmax(500, 'Da', 0.005), 500.0050000001, 'Works with \'500, Da, 0.005\' for maximum'); | |
83 #21 | |
84 is ( mz_delta_conversion_Testmin(100, 'ppm', 5), 99.9995, 'Works with \'100, ppm, 5\' for minimum'); | |
85 #22 | |
86 is ( mz_delta_conversion_Testmax(100, 'ppm', 5), 100.0005000001, 'Works with \'100, ppm, 5\' for maximum'); | |
87 #23 | |
88 is ( mz_delta_conversion_Testmin(500, 'ppm', 5), 499.9975, 'Works with \'500, ppm, 5\' for minimum'); | |
89 #24 | |
90 is ( mz_delta_conversion_Testmax(500, 'ppm', 5), 500.0025000001, 'Works with \'500, ppm, 5\' for maximum'); | |
91 print "\n--\n" ; | |
92 | |
93 ## testing dichotomi_search | |
94 print "\n-- Test dichotomi_search lib\n\n" ; | |
95 #25 | |
96 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '0'), -1, 'Works with \'0\' smaller than the 1st element'); | |
97 #26 | |
98 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '1'), 0, 'Works with \'1\' equal to the 1st element'); | |
99 #27 | |
100 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '5'), 4, 'Works with \'5\' equal to the 4th element'); | |
101 #28 | |
102 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '11'), 10, 'Works with \'11\' equal to the last (10th) element'); | |
103 #29 | |
104 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '11.001'), 11, 'Works with \'11.001\' greater than the last (10th) element'); | |
105 #30 | |
106 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '9.5'), 9, 'Works with \'9.5\' between the 9th and the 10th element return \'9\'(the index of the 10th)'); | |
107 #31 | |
108 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '8.5'), 8, 'Works with \'8.5\' between the 8th and the 9th element return \'8\'(the index of the 9th)'); | |
109 #32 | |
110 is ( dichotomi_search_Test(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11'], '10.5'), 10, 'Works with \'10.5\' between the 10th and the 11th element return \'10\'(the index of the 11th)'); | |
111 print "\n--\n" ; | |
112 | |
113 ## test of input bank parsing | |
114 print "\n-- Test bank parsing\n\n" ; | |
115 is_deeply ( parse_bank_interest_Test( | |
116 '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/tool-bank_inhouse/test_data/in_test2.tabular', 1), | |
117 { '422.0849114' => [ [ 'C19H18O11', '422.0849114' ] ], '98.952389' => [ [ 'Halothane', '98.952389' ] ], '209.987659' => [ [ 'Bismuth', '209.987659' ] ], '18.0105647' => [ [ 'H2O', '18.0105647' ] ], '199.951068' => [ [ 'Picolinic acid', '199.951068' ] ], '535.3181236' => [ [ 'C18H45N7O11', '535.3181236' ] ] }, | |
118 "Parsing a bank method works an return a well organized hash\n" ) ; | |
119 | |
120 print "\n--\n" ; | |
121 | |
122 | |
123 ## test of rest ws of PeakForest | |
124 print "\n-- Test PeakForest WS\n\n" ; | |
125 is_deeply ( db_pforest_get_clean_range_Test( | |
126 'https://rest.peakforest.org', '/spectra/lcms/peaks/get-range-clean', '190.0', '200.0', 'negative'), | |
127 [{ 'cpds' => [ 186 ], 'thMass' => '195.0877', 'sp' => 25, 'ri' => '100', 'deltaPPM' => '0.245', 'composition' => 'C8H11N4O2', 'attribution' => '[M+H]+', 'mz' => '195.0875' }, { 'composition' => 'C9H9O5', 'attribution' => '[M-H]-', 'ri' => '100', 'deltaPPM' => '0.271', 'cpds' => [ 360 ], 'thMass' => '197.0456', 'sp' => 37, 'mz' => '197.0452' }, { 'composition' => 'C9H12NO4', 'attribution' => '[M+H]+', 'deltaPPM' => '-0.426098891623529', 'ri' => '100', 'thMass' => '198.0760844', 'sp' => 77, 'cpds' => [ 1841 ], 'mz' => '198.076' }, { 'mz' => '196.0614', 'composition' => 'C9H10NO4', 'attribution' => '[M-H]-', 'cpds' => [ 1841 ], 'thMass' => '196.0615311', 'sp' => 78, 'ri' => '100', 'deltaPPM' => '-0.668667633415113' }, { 'cpds' => [ 1841 ], 'thMass' => '198.0760844', 'sp' => 79, 'ri' => '100', 'deltaPPM' => '-0.426098891623529', 'composition' => 'C9H12NO4', 'attribution' => '[M+H]+', 'mz' => '198.076' }], | |
128 "PForest WS call works an return a clean range og mz between 190 and 200\n" ) ; | |
129 | |
130 print "\n--\n" ; | |
131 | |
132 ## test of rest ws of PeakForest | |
133 print "\n-- Test PeakForest JSON Bank parsing\n\n" ; | |
134 | |
135 my ($bank, $headers) = map_pfjson_bankobject_Test([ { 'cpds' => [ 186 ], 'mz' => '195.0875' }, {'mz' => '198.076', 'cpds' => [ 190 ]} ]) ; | |
136 is_deeply ( | |
137 $bank, | |
138 { '198.076' => [ [ 190, '198.076' ] ], '195.0875' => [ [ 186, '195.0875' ] ] }, | |
139 "Parsing json bank from PeakForest works an return a well organized hash for data\n" ) ; | |
140 | |
141 is_deeply ( | |
142 $headers, | |
143 ['id', 'mz'], | |
144 "Parsing json bank from PeakForest works an return a well organized array for headers\n" ) ; |