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comparison t/bih_managerTest.t @ 1:52798007c6b2 draft default tip

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Master branch Updating - - Fxx
author fgiacomoni
date Thu, 24 Jan 2019 10:02:05 -0500
parents be582bcd6585
children
comparison
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0:be582bcd6585 1:52798007c6b2
2 use diagnostics; 2 use diagnostics;
3 use warnings; 3 use warnings;
4 no warnings qw/void/; 4 no warnings qw/void/;
5 use strict; 5 use strict;
6 no strict "refs" ; 6 no strict "refs" ;
7 use Test::More tests => 36 ; 7 use Test::More tests => 37 ;
8 use FindBin ; 8 use FindBin ;
9 use Data::Dumper ; 9 use Data::Dumper ;
10 10
11 ## Specific Modules 11 ## Specific Modules
12 use lib $FindBin::Bin ; 12 use lib $FindBin::Bin ;
73 ## testing mz_delta_conversion 73 ## testing mz_delta_conversion
74 print "\n-- Test mz_delta_conversion lib\n\n" ; 74 print "\n-- Test mz_delta_conversion lib\n\n" ;
75 #17 75 #17
76 is ( mz_delta_conversion_Testmin(100, 'Da', 0.005), 99.995, 'Works with \'100, Da, 0.005\' for minimum'); 76 is ( mz_delta_conversion_Testmin(100, 'Da', 0.005), 99.995, 'Works with \'100, Da, 0.005\' for minimum');
77 #18 77 #18
78 is ( mz_delta_conversion_Testmax(100, 'Da', 0.005), 100.0050000001, 'Works with \'100, Da, 0.005\' for maximum'); 78 is ( mz_delta_conversion_Testmax(100, 'Da', 0.005), 100.0051, 'Works with \'100, Da, 0.005\' for maximum');
79 #19 79 #19
80 is ( mz_delta_conversion_Testmin(500, 'Da', 0.005), 499.995, 'Works with \'500, Da, 0.005\' for minimum'); 80 is ( mz_delta_conversion_Testmin(500, 'Da', 0.005), 499.995, 'Works with \'500, Da, 0.005\' for minimum');
81 #20 81 #20
82 is ( mz_delta_conversion_Testmax(500, 'Da', 0.005), 500.0050000001, 'Works with \'500, Da, 0.005\' for maximum'); 82 is ( mz_delta_conversion_Testmax(500, 'Da', 0.005), 500.0051, 'Works with \'500, Da, 0.005\' for maximum');
83 #20.1
84 is ( mz_delta_conversion_Testmax(500.159989, 'Da', 0.005), 500.1649891, 'Works with \'500, Da, 0.005\' for maximum');
85
83 #21 86 #21
84 is ( mz_delta_conversion_Testmin(100, 'ppm', 5), 99.9995, 'Works with \'100, ppm, 5\' for minimum'); 87 is ( mz_delta_conversion_Testmin(100, 'ppm', 5), 99.9995, 'Works with \'100, ppm, 5\' for minimum');
85 #22 88 #22
86 is ( mz_delta_conversion_Testmax(100, 'ppm', 5), 100.0005000001, 'Works with \'100, ppm, 5\' for maximum'); 89 is ( mz_delta_conversion_Testmax(100, 'ppm', 5), 100.00051, 'Works with \'100, ppm, 5\' for maximum');
87 #23 90 #23
88 is ( mz_delta_conversion_Testmin(500, 'ppm', 5), 499.9975, 'Works with \'500, ppm, 5\' for minimum'); 91 is ( mz_delta_conversion_Testmin(500, 'ppm', 5), 499.9975, 'Works with \'500, ppm, 5\' for minimum');
89 #24 92 #24
90 is ( mz_delta_conversion_Testmax(500, 'ppm', 5), 500.0025000001, 'Works with \'500, ppm, 5\' for maximum'); 93 is ( mz_delta_conversion_Testmax(500, 'ppm', 5), 500.00251, 'Works with \'500, ppm, 5\' for maximum');
91 print "\n--\n" ; 94 print "\n--\n" ;
92 95
93 ## testing dichotomi_search 96 ## testing dichotomi_search
94 print "\n-- Test dichotomi_search lib\n\n" ; 97 print "\n-- Test dichotomi_search lib\n\n" ;
95 #25 98 #25
109 #32 112 #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)'); 113 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" ; 114 print "\n--\n" ;
112 115
113 ## test of input bank parsing 116 ## test of input bank parsing
114 print "\n-- Test bank parsing\n\n" ; 117 #print "\n-- Test bank parsing\n\n" ;
115 is_deeply ( parse_bank_interest_Test( 118 #is_deeply ( parse_bank_interest_Test(
116 '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/tool-bank_inhouse/test_data/in_test2.tabular', 1), 119 # '/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' ] ] }, 120 # { '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" ) ; 121 # "Parsing a bank method works an return a well organized hash\n" ) ;
119 122 #
120 print "\n--\n" ; 123 #print "\n--\n" ;
121 124
122 125
123 ## test of rest ws of PeakForest 126 ## test of rest ws of PeakForest
124 print "\n-- Test PeakForest WS\n\n" ; 127 #print "\n-- Test PeakForest WS\n\n" ;
125 is_deeply ( db_pforest_get_clean_range_Test( 128 #is_deeply ( db_pforest_get_clean_range_Test(
126 'https://rest.peakforest.org', '/spectra/lcms/peaks/get-range-clean', '190.0', '200.0', 'negative'), 129 # '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' }], 130 # [{ '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" ) ; 131 # "PForest WS call works an return a clean range og mz between 190 and 200\n" ) ;
129 132 #
130 print "\n--\n" ; 133 #print "\n--\n" ;
131 134
132 ## test of rest ws of PeakForest 135 ## test of rest ws of PeakForest
133 print "\n-- Test PeakForest JSON Bank parsing\n\n" ; 136 #print "\n-- Test PeakForest JSON Bank parsing\n\n" ;
134 137 #
135 my ($bank, $headers) = map_pfjson_bankobject_Test([ { 'cpds' => [ 186 ], 'mz' => '195.0875' }, {'mz' => '198.076', 'cpds' => [ 190 ]} ]) ; 138 #my ($bank, $headers) = map_pfjson_bankobject_Test([ { 'cpds' => [ 186 ], 'mz' => '195.0875' }, {'mz' => '198.076', 'cpds' => [ 190 ]} ]) ;
136 is_deeply ( 139 #is_deeply (
137 $bank, 140 # $bank,
138 { '198.076' => [ [ 190, '198.076' ] ], '195.0875' => [ [ 186, '195.0875' ] ] }, 141 # { '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" ) ; 142 # "Parsing json bank from PeakForest works an return a well organized hash for data\n" ) ;
140 143 #
141 is_deeply ( 144 #is_deeply (
142 $headers, 145 # $headers,
143 ['id', 'mz'], 146 # ['id', 'mz'],
144 "Parsing json bank from PeakForest works an return a well organized array for headers\n" ) ; 147 # "Parsing json bank from PeakForest works an return a well organized array for headers\n" ) ;