Mercurial > repos > fgiacomoni > bank_inhouse
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/t/bih_managerTest.t Thu Oct 04 10:37:14 2018 -0400 @@ -0,0 +1,144 @@ +#! perl +use diagnostics; +use warnings; +no warnings qw/void/; +use strict; +no strict "refs" ; +use Test::More tests => 36 ; +use FindBin ; +use Data::Dumper ; + +## Specific Modules +use lib $FindBin::Bin ; +my $binPath = $FindBin::Bin ; +use lib::bihTest qw( :ALL ) ; + +## testing check_interval +print "\n-- test whether a value is in the interval defines\n\n" ; +#01 +is ( check_interval_Test('test', '0', '1'), "'test' isn't a valid number!", 'Works with a value that is not a number'); +#02 +is ( check_interval_Test('', '0', '1'), "'' isn't a valid number!", 'Works with a value that is not a number'); +#03 +is ( check_interval_Test('-0.5', '-1', '0'), "OK", 'Works with a negative float'); +#04 +is ( check_interval_Test('-0.5', '0', '1'), "'-0.5' is below the minimum!", 'Works with a number below the minimum!'); +#05 +is ( check_interval_Test('2', '0', '1'), "'2' is greater than the maximum!", 'Works with a number greater than the maximum!'); +print "\n--\n" ; + +## testing format_manual_masses +print "\n-- Test format manual list of values lib for values (ex=> masses)\n\n" ; +#06 +isa_ok( format_manual_list_values_Testvalues('562.0235', ' '), 'ARRAY' ); +#07 +is_deeply(format_manual_list_values_Testvalues('562.0235', ' '), [562.0235], 'Works with \'562.0235\' for mass'); +#08 +is_deeply(format_manual_list_values_Testvalues('562.0235 987.4568', ' '), [562.0235, 987.4568], 'Works with \'562.0235 987.4568\' for masses'); +#09 +is_deeply(format_manual_list_values_Testvalues('562.0235;987.4568', ';'), [562.0235, 987.4568], 'Works with \'562.0235;987.4568\' for masses'); +print "\n--\n" ; + +print "\n-- Test format manual list of values lib for ids\n\n" ; +#10 +isa_ok( format_manual_list_values_Testids('562.0235', ' '), 'ARRAY' ); +#11 +is_deeply(format_manual_list_values_Testids('562.0235', ' '), ['value_1'], 'Works with \'562.0235\' for ids'); +#12 +is_deeply(format_manual_list_values_Testids('562.0235 987.4568', ' '), ['value_1', 'value_2'], 'Works with \'562.0235 987.4568\' for ids'); +#13 +is_deeply(format_manual_list_values_Testids('562.0235 987.4568 ', ' '), ['value_1', 'value_2'], 'Works with \'562.0235 987.4568 \' for ids'); +#14 +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'); +#15 +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'); +#16 +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'); +print "\n--\n" ; + +## testing manage_mode +#print "\n-- Test manage_mode lib\n\n" ; +#09 +#isa_ok( manage_mode_Testionization('positive,negative,neutral'), 'ARRAY' ); +#10 +#is_deeply(manage_mode_Testionization('positive,negative,neutral'), ['positive', 'negative', 'neutral'], 'Works with \'562.0235\' for ids'); +#14 +#isa_ok( format_manual_list_values_Testids('562.0235 987.4568'), 'ARRAY' ); +#15 +#is_deeply(format_manual_list_values_Testids('562.0235 987.4568'), ['mass_1', 'mass_2'], 'Works with \'562.0235 987.4568\' for ids'); +#16 +#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'); +#print "\n--\n" ; + +## testing mz_delta_conversion +print "\n-- Test mz_delta_conversion lib\n\n" ; +#17 +is ( mz_delta_conversion_Testmin(100, 'Da', 0.005), 99.995, 'Works with \'100, Da, 0.005\' for minimum'); +#18 +is ( mz_delta_conversion_Testmax(100, 'Da', 0.005), 100.0050000001, 'Works with \'100, Da, 0.005\' for maximum'); +#19 +is ( mz_delta_conversion_Testmin(500, 'Da', 0.005), 499.995, 'Works with \'500, Da, 0.005\' for minimum'); +#20 +is ( mz_delta_conversion_Testmax(500, 'Da', 0.005), 500.0050000001, 'Works with \'500, Da, 0.005\' for maximum'); +#21 +is ( mz_delta_conversion_Testmin(100, 'ppm', 5), 99.9995, 'Works with \'100, ppm, 5\' for minimum'); +#22 +is ( mz_delta_conversion_Testmax(100, 'ppm', 5), 100.0005000001, 'Works with \'100, ppm, 5\' for maximum'); +#23 +is ( mz_delta_conversion_Testmin(500, 'ppm', 5), 499.9975, 'Works with \'500, ppm, 5\' for minimum'); +#24 +is ( mz_delta_conversion_Testmax(500, 'ppm', 5), 500.0025000001, 'Works with \'500, ppm, 5\' for maximum'); +print "\n--\n" ; + +## testing dichotomi_search +print "\n-- Test dichotomi_search lib\n\n" ; +#25 +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'); +#26 +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'); +#27 +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'); +#28 +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'); +#29 +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'); +#30 +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)'); +#31 +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)'); +#32 +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)'); +print "\n--\n" ; + +## test of input bank parsing +print "\n-- Test bank parsing\n\n" ; +is_deeply ( parse_bank_interest_Test( + '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/tool-bank_inhouse/test_data/in_test2.tabular', 1), + { '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' ] ] }, + "Parsing a bank method works an return a well organized hash\n" ) ; + +print "\n--\n" ; + + +## test of rest ws of PeakForest +print "\n-- Test PeakForest WS\n\n" ; +is_deeply ( db_pforest_get_clean_range_Test( + 'https://rest.peakforest.org', '/spectra/lcms/peaks/get-range-clean', '190.0', '200.0', 'negative'), + [{ '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' }], + "PForest WS call works an return a clean range og mz between 190 and 200\n" ) ; + +print "\n--\n" ; + +## test of rest ws of PeakForest +print "\n-- Test PeakForest JSON Bank parsing\n\n" ; + +my ($bank, $headers) = map_pfjson_bankobject_Test([ { 'cpds' => [ 186 ], 'mz' => '195.0875' }, {'mz' => '198.076', 'cpds' => [ 190 ]} ]) ; +is_deeply ( + $bank, + { '198.076' => [ [ 190, '198.076' ] ], '195.0875' => [ [ 186, '195.0875' ] ] }, + "Parsing json bank from PeakForest works an return a well organized hash for data\n" ) ; + +is_deeply ( + $headers, + ['id', 'mz'], + "Parsing json bank from PeakForest works an return a well organized array for headers\n" ) ; \ No newline at end of file