Mercurial > repos > fgiacomoni > massbank_ws_searchspectrum
view t/massbank_ws_searchspectrum_Test.t @ 0:023c380900ef draft default tip
Init repository with last massbank_ws_searchspectrum master version
| author | fgiacomoni |
|---|---|
| date | Wed, 19 Apr 2017 11:31:58 -0400 |
| parents | |
| children |
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#! perl use diagnostics; use warnings; no warnings qw/void/; use strict; no strict "refs" ; use Test::More qw( no_plan ); #use Test::More tests => 8 ; ## with MAPPER SEQUENCE use FindBin ; use Carp ; ## Specific Modules use lib $FindBin::Bin ; my $binPath = $FindBin::Bin ; use lib::massbank_api_Test qw( :ALL ) ; use lib::massbank_mapper_Test qw( :ALL ) ; use lib::massbank_main_Test qw( :ALL ) ; ## To launch the right sequence : MAIN, API, MAPPER, THREADER, COMPUTE... my $sequence = 'COMPUTE' ; my $current_test = 1 ; my $server = 'EU' ; if ($sequence eq "COMPUTE") { print "\n\t\t\t\t * * * * * * \n" ; print "\t * * * - - - Test MassBank Main script - - - * * * \n\n" ; sleep 1 ; print "\n** Test $current_test min_from_double_with_delta with doubles **\n" ; $current_test++ ; is_deeply( min_from_double_with_deltaTest ( 303.0485467, 'Da', 0.01), 303.0385467, 'Method \'min_and_max_from_double_with_delta\' works with a double and return the attended min value'); sleep 1 ; print "\n** Test $current_test max_from_double_with_delta with doubles **\n" ; $current_test++ ; is_deeply( max_from_double_with_deltaTest ( 303.0485467, 'Da', 0.01), 303.0585467001, 'Method \'max_from_double_with_delta\' works with a double and return the attended max value'); } elsif ($sequence eq "MAIN") { print "\n\t\t\t\t * * * * * * \n" ; print "\t * * * - - - Test MassBank Main script - - - * * * \n\n" ; ## Test NORMAL file => OK ok( run_main_massbank_pl( '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/pcgrp_annot.tsv', 1, 14, 7, 1, 0.5, 'Positive', 'all', 2, 'unit', 0.3, 5, 'EU', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out1.json', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out1.csv', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out1.xls'), 'Main script massbank_ws_searchspectrum.pl with is running and manage normal data (mz, ) ' ); ## Test BUG file wih relative intensities => OK ok( run_main_massbank_pl( '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/261-pcgroups-mz-relative_int.tsv', '2', '1', '3', '1', 0.5, 'Positive', 'all', 2, 'unit', 0.3, 5, 'JP', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out2.json', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out2.csv', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out2.xls'), 'Main script massbank_ws_searchspectrum.pl with is running and manage real file (mz, relative int, ...)' ); ## Test BUG file wih real intensities (>10000) => OK ok( run_main_massbank_pl( '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/2214-mz-int-pcgroups.tsv', '1', '3', '2', '1', 0.5, 'Positive', 'all', 2, 'unit', 0.3, 5, 'JP', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out3.json', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out3.csv', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out3.xls'), 'Main script massbank_ws_searchspectrum.pl with is running and manage real file (mz, relative int, ...)' ); ## Test BUG file wih relative intensities and ppm / 15 / 5 => OK ok( run_main_massbank_pl( '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/261-pcgroups-mz-relative_int.tsv', '2', '1', '3', '1', 0.5, 'Positive', 'all', 2, 'ppm', 15, 5, 'JP', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out4.json', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out4.csv', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out4.xls'), 'Main script massbank_ws_searchspectrum.pl with is running and manage real file (mz, relative int, ...)' ); ## Test BUG file wih real intensities (>10000) and ppm / 15 / 5 + long file => OK ok( run_main_massbank_pl( '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/2214-mz-int-pcgroups.tsv', '1', '3', '2', '1', 0.5, 'Positive', 'all', 2, 'ppm', 15, 5, 'JP', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out5.json', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out5.csv', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out5.xls'), 'Main script massbank_ws_searchspectrum.pl with is running and manage real file (mz, int, ...)' ); ## Test BUG file wih real intensities (>10000) and ppm / 15 / 5 + long file -> parameters c5b5ac363f7bdb2d => OK ok( run_main_massbank_pl( '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/2214-mz-int-pcgroups.tsv', '1', '3', '2', '1', 0.5, 'Positive', "LC-ESI-IT,LC-ESI-ITFT,LC-ESI-ITTOF,LC-ESI-Q,LC-ESI-QFT,LC-ESI-QIT,LC-ESI-QQ,LC-ESI-QTOF,LC-ESI-TOF", 10, 'ppm', 15, 5, 'JP', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out6.json', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out6.csv', '/Users/fgiacomoni/Inra/labs/tests/massbank_V02/out6.xls'), 'Main script massbank_ws_searchspectrum.pl with is running and manage real file (mz, int, ...)' ); } #-masses #-col_mz 1 #-col_pcgroup 14 #-col_int 7 #-lineheader 1 #-mode Positive #-instruments all #-max 2 #-unit unit #-tolerance 0.3 #-cutoff 5 #-server JP #-json /Users/fgiacomoni/Inra/labs/tests/massbank_V02/out.json #-csv /Users/fgiacomoni/Inra/labs/tests/massbank_V02/out.csv #-xls /Users/fgiacomoni/Inra/labs/tests/massbank_V02/out.xls elsif ($sequence eq "MAPPER") { ## testing mapper module of massbank wrapper. ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n\t\t\t\t * * * * * * \n" ; print "\t * * * - - - Test MassBank Mapper module - - - * * * \n\n" ; ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $pcs, $mzs, $ints sleep 1 ; print "\n** Test $current_test get_pcgroup_list with pcs array **\n" ; $current_test++ ; is_deeply( get_pcgroup_listTest ( [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,7,8,8,8,8,8,9,9,10,10,10,10,11,12,13,13,13,14,14,14] ), ['1', '2','3','4','5','6','7','8','9','10','11','12','13','14'] , 'Method \'getPcgroupList\' works with various and multiple pcgroups and return the attended uniq pcgroups array'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $pcs, $mzs, $ints print "\n** Test $current_test get_pcgroups with pcs, mzs, ints arrays **\n" ; $current_test++ ; is_deeply( get_pcgroupsTest ( [1, 2, 1, 2, 1, 2, 1], ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['300', '300', '300', '300', '300', '300', '300'] ), { '1' => { 'id' => '1', 'mzmed' => ['273.096','290.118','292.113','580.179'], 'into' => ['300','300','300','300'], 'annotation' => {}, 'massbank_ids' => [] }, '2' => { 'annotation' => {}, 'into' => ['300','300','300'], 'mzmed' => ['289.086','291.096','579.169'], 'id' => '2', 'massbank_ids' => [], } }, 'Method \'getPcgroups\' works with two pcgroups and return the attended pcgroups object'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $pcs, $mzs, $ints print "\n** Test $current_test get_pcgroups with pcs, mzs, ints (some can be equal to 0) arrays **\n" ; $current_test++ ; is_deeply( get_pcgroupsTest ( [1, 2, 1, 2, 1, 2, 1], ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['0', '300', '300', '300', '300', '300', '300'] ), { '1' => { 'id' => '1', 'mzmed' => ['273.096','290.118','292.113','580.179'], 'into' => ['0','300','300','300'], 'annotation' => {}, 'massbank_ids' => [] }, '2' => { 'annotation' => {}, 'into' => ['300','300','300'], 'mzmed' => ['289.086','291.096','579.169'], 'id' => '2', 'massbank_ids' => [], } }, 'Method \'getPcgroups\' works with two pcgroups (with intensity equal to 0) and return the attended pcgroups object'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $header, $init_pcs, $pcgroups sleep 1 ; print "\n** Test $current_test set_massbank_matrix_object with pc array and pcgroups object **\n" ; $current_test++ ; is_deeply( set_massbank_matrix_objectTest ( 'massbank', [1,1,2,2,1], { '1' => { 'id' => '1', 'mzmed' => ['273.096','290.118','292.113','580.179'], 'into' => ['300','300','300','300'], 'annotation' => {'num_res' => 3}, 'massbank_ids' => ['CA0001', 'CA0011', 'CA0111'] }, '2' => { 'annotation' => {'num_res' => 3}, 'into' => ['300','300','300'], 'mzmed' => ['289.086','291.096','579.169'], 'id' => '2', 'massbank_ids' => ['CA0002', 'CA0022', 'CA0222'], } } ), ## end argvts [ [ 'massbank' ], ['CA0001|CA0011|CA0111'],['CA0001|CA0011|CA0111'], ['CA0002|CA0022|CA0222'], ['CA0002|CA0022|CA0222'], ['CA0001|CA0011|CA0111'] ], 'Method \'set_massbank_matrix_object\' works with header, pcs list, pcgroups and return the attended massbank matrix'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $header, $init_pcs, $pcgroups sleep 1 ; print "\n** Test $current_test set_massbank_matrix_object with undef hearder, pc array and pcgroups object **\n" ; $current_test++ ; is_deeply( set_massbank_matrix_objectTest ( undef, [1,1,2,2,1], { '1' => { 'id' => '1', 'mzmed' => ['273.096','290.118','292.113','580.179'], 'into' => ['300','300','300','300'], 'annotation' => {'num_res' => 3}, 'massbank_ids' => ['CA0001', 'CA0011', 'CA0111'] }, '2' => { 'annotation' => {'num_res' => 3}, 'into' => ['300','300','300'], 'mzmed' => ['289.086','291.096','579.169'], 'id' => '2', 'massbank_ids' => ['CA0002', 'CA0022', 'CA0222'], } } ), ## end argvts [ ['CA0001|CA0011|CA0111'],['CA0001|CA0011|CA0111'], ['CA0002|CA0022|CA0222'], ['CA0002|CA0022|CA0222'], ['CA0001|CA0011|CA0111'] ], 'Method \'set_massbank_matrix_object\' works with undef header and return the attended massbank matrix'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $header, $init_pcs, $pcgroups sleep 1 ; print "\n** Test $current_test set_massbank_matrix_object with empty massbankIds **\n" ; $current_test++ ; is_deeply( set_massbank_matrix_objectTest ( 'massbank', [1,1,2,2,1], { '1' => { 'id' => '1', 'mzmed' => ['273.096','290.118','292.113','580.179'], 'into' => ['300','300','300','300'], 'annotation' => {'num_res' => 3}, 'massbank_ids' => ['CA0001', 'CA0011', 'CA0111'] }, '2' => { 'annotation' => {'num_res' => 0}, 'into' => ['300','300','300'], 'mzmed' => ['289.086','291.096','579.169'], 'id' => '2', 'massbank_ids' => [], } } ), ## end argvts [ [ 'massbank' ], ['CA0001|CA0011|CA0111'],['CA0001|CA0011|CA0111'], ['No_result_found_on_MassBank'], ['No_result_found_on_MassBank'], ['CA0001|CA0011|CA0111'] ], 'Method \'set_massbank_matrix_object\' works with empty massbank_ids and return the attended massbank matrix'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $input_matrix_object, $massbank_matrix_object sleep 1 ; print "\n** Test $current_test add_massbank_matrix_to_input_matrix with two matrix **\n" ; $current_test++ ; is_deeply( add_massbank_matrix_to_input_matrixTest ( [[ 'pcgroup' ],[1],[1],[2],[2],[1]], [ [ 'massbank' ], ['CA0001|CA0011|CA0111'],['CA0001|CA0011|CA0111'], ['CA0002|CA0022|CA0222'], ['CA0002|CA0022|CA0222'], ['CA0001|CA0011|CA0111'] ], ), ## end argvts [ ['pcgroup','massbank'],[1,'CA0001|CA0011|CA0111'],[1,'CA0001|CA0011|CA0111'],[2,'CA0002|CA0022|CA0222'],[2,'CA0002|CA0022|CA0222'],[1,'CA0001|CA0011|CA0111'] ], ## end results 'Method \'add_massbank_matrix_to_input_matrix\' works with two wel formatted matrix and return the right csv matrix'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $pcgroups_object, threshold sleep 1 ; print "\n** Test $current_test filter_pcgroup_res with pcgroups object and a threshold **\n" ; $current_test++ ; is_deeply( filter_pcgroup_resTest ( { '1' => { 'massbank_ids' => ['MB0004', 'MB0005', 'MB0008'], 'annotation' => {'res' => [ {'score' => 0.4, 'id' => 'MB0004'}, {'score' => 0.8, 'id' => 'MB0008' }, {'score' => 0.5, 'id' => 'MB0005' } ], 'num_res' => 3 } }, '2' => { 'massbank_ids' => ['MB0004', 'MB0008', 'MB0007'], 'annotation' => {'res' => [{'score' => 0.4, 'id' => 'MB0004'}, {'score' => 0.8, 'id' => 'MB0008'}, {'score' => 0.7, 'id' => 'MB0007'} ], 'num_res' => 3 } } }, 0.5 ), ## end argvts { '1' => { 'massbank_ids' => ['MB0005', 'MB0008'], 'annotation' => { 'res' => [ {'score' => 0.5, 'id' => 'MB0005' }, {'score' => 0.8, 'id' => 'MB0008'} ], 'num_res' => 2 } }, '2' => { 'massbank_ids' => ['MB0007', 'MB0008'], 'annotation' => {'res' => [{'score' => 0.7, 'id' => 'MB0007' }, {'score' => 0.8, 'id' => 'MB0008' } ], 'num_res' => 2 } } }, ## end results 'Method \'filter_pcgroup_resTest\' works with well formated pcgroups object and a float for threshold'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $pcgroups_object, threshold sleep 1 ; print "\n** Test $current_test filter_pcgroup_res with empty pcgroups object and a threshold **\n" ; $current_test++ ; is_deeply( filter_pcgroup_resTest ( { '1' => { 'massbank_ids' => [], 'annotation' => {'res' => [ ], 'num_res' => 1 } }, '2' => { 'massbank_ids' => [], 'annotation' => {'res' => [ ], 'num_res' => 1 } } }, 0.5 ), ## end argvts { '1' => { 'massbank_ids' => [], 'annotation' => { 'res' => [ ], 'num_res' => 0 } }, '2' => { 'massbank_ids' => [], 'annotation' => {'res' => [ ], 'num_res' => 0 } } }, ## end results 'Method \'filter_pcgroup_resTest\' works with an empty pcgroups object and a float for threshold'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $pcgroups_object, threshold sleep 1 ; print "\n** Test $current_test filter_pcgroup_res with pcgroups object but undef params and a threshold **\n" ; $current_test++ ; is_deeply( filter_pcgroup_resTest ( { '1' => { 'massbank_ids' => [], 'annotation' => {'res' => [ {'score' => undef, 'id' => undef} ], 'num_res' => 0 } }, '2' => { 'massbank_ids' => ['MB0004', 'MB0008', 'MB0007'], 'annotation' => {'res' => [{'score' => 0.4, 'id' => 'MB0004'}, {'score' => 0.8, 'id' => 'MB0008'}, {'score' => 0.7, 'id' => 'MB0007'} ], 'num_res' => 3 } } }, 0.5 ), ## end argvts { '1' => { 'massbank_ids' => [], 'annotation' => { 'res' => [ {'score' => undef, 'id' => undef } ], 'num_res' => 0 } }, '2' => { 'massbank_ids' => ['MB0007', 'MB0008'], 'annotation' => {'res' => [{'score' => 0.7, 'id' => 'MB0007' }, {'score' => 0.8, 'id' => 'MB0008' } ], 'num_res' => 2 } } }, ## end results 'Method \'filter_pcgroup_resTest\' works with well formated pcgroups object (but undef value) and a float for threshold'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $pcgroups_object sleep 1 ; print "\n** Test $current_test compute_ids_from_pcgroups_res with pcgroups object **\n" ; $current_test++ ; is_deeply( compute_ids_from_pcgroups_resTest ( { '1' => { 'massbank_ids' => ['MB0004', 'MB0005', 'MB0008'], 'annotation' => {'res' => [ {'score' => 0.4, 'id' => 'MB0004'}, {'score' => 0.8, 'id' => 'MB0008' }, {'score' => 0.5, 'id' => 'MB0005' } ], 'num_res' => 3 } }, '2' => { 'massbank_ids' => ['MB0004', 'MB0008', 'MB0007'], 'annotation' => {'res' => [{'score' => 0.4, 'id' => 'MB0004'}, {'score' => 0.8, 'id' => 'MB0008'}, {'score' => 0.7, 'id' => 'MB0007'} ], 'num_res' => 3 } } }, ), ## end argvts ['MB0004', 'MB0005', 'MB0007', 'MB0008'], ## end results 'Method \'compute_ids_from_pcgroups_res\' works with a classic pcgroups object return a nice and unique list of ids'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## ARGVTS : $massbank_ids, chunk_size sleep 1 ; print "\n** Test $current_test get_massbank_records_by_chunk with ids list **\n" ; $current_test++ ; is_deeply( get_massbank_records_by_chunkTest ( 'EU', ['KOX00002', 'KOX00003', 'FU000001', 'TY000040', 'TY000041', 'FU000002'], 2 ), ## end argvts ['ACCESSION: KOX00002 RECORD_TITLE: GABA; LC-ESI-QTOF; MS2; MERGED; [M+H]+ DATE: 2011.08.24 (Created 2008.11.28) AUTHORS: Institute for Advanced Biosciences, Keio Univ. LICENSE: Copyright 2006-2011 Keio COMMENT: Peak data in the following records are not open to the public as requested by their authors. COMMENT: Instead MassBank provides the merged spectra for the public. COMMENT: This record was generated by merging the following three MassBank records. COMMENT: [Merging] KO006374 GABA; LC-ESI-QTOF; MS2; CE:10 V [M+H]+ COMMENT: [Merging] KO006375 GABA; LC-ESI-QTOF; MS2; CE:20 V [M+H]+ COMMENT: [Merging] KO006376 GABA; LC-ESI-QTOF; MS2; CE:30 V [M+H]+ COMMENT: [Merging] KO006377 GABA; LC-ESI-QTOF; MS2; CE:40 V [M+H]+ COMMENT: [Merging] KO006378 GABA; LC-ESI-QTOF; MS2; CE:50 V [M+H]+ CH$NAME: GABA CH$NAME: 4-Aminobutanoate CH$NAME: 4-Aminobutanoic acid CH$NAME: 4-Aminobutylate CH$NAME: 4-Aminobutyrate CH$NAME: 4-Aminobutyric acid CH$NAME: gamma-Aminobutyric acid CH$COMPOUND_CLASS: N/A CH$FORMULA: C4H9NO2 CH$EXACT_MASS: 103.06333 CH$SMILES: NCCCC(O)=O CH$IUPAC: InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) CH$LINK: CAS 56-12-2 CH$LINK: CHEBI 30566 CH$LINK: KEGG C00334 CH$LINK: NIKKAJI J1.375G CH$LINK: PUBCHEM SID:3628 AC$INSTRUMENT: Qstar, Applied Biosystems AC$INSTRUMENT_TYPE: LC-ESI-QTOF AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE POSITIVE MS$FOCUSED_ION: PRECURSOR_M/Z 104 MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+ PK$ANNOTATION: 39.0234750963 45.0340397826 68.0500241978 69.0340397826 86.0605888841 87.0446044689 104.0711535704 PK$NUM_PEAK: N/A PK$PEAK: m/z int. rel.int. N/A ', 'ACCESSION: KOX00003 RECORD_TITLE: Adenosine; LC-ESI-QTOF; MS2; MERGED; [M-H]- DATE: 2012.05.21 (Created 2008.11.28) AUTHORS: Institute for Advanced Biosciences, Keio Univ. LICENSE: Copyright 2006-2011 Keio COMMENT: Peak data in the following records are not open to the public as requested by their authors. COMMENT: Instead MassBank provides the merged spectra for the public. COMMENT: This record was generated by merging the following three MassBank records. COMMENT: [Merging] KO004298 Adenosine; LC-ESI-QTOF; MS2; CE:10 V [M-H]- COMMENT: [Merging] KO004299 Adenosine; LC-ESI-QTOF; MS2; CE:20 V [M-H]- COMMENT: [Merging] KO004301 Adenosine; LC-ESI-QTOF; MS2; CE:40 V [M-H]- COMMENT: [Merging] KO004302 Adenosine; LC-ESI-QTOF; MS2; CE:50 V [M-H]- CH$NAME: Adenosine CH$COMPOUND_CLASS: N/A CH$FORMULA: C10H13N5O4 CH$EXACT_MASS: 267.09675 CH$SMILES: OC[C@@H](O1)[C@@H](O)[C@@H](O)[C@@H]1n(c3)c(n2)c(n3)c(N)nc2 CH$IUPAC: InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1 CH$LINK: CAS 58-61-7 CH$LINK: CHEBI 16335 CH$LINK: CHEMPDB ADN CH$LINK: KEGG C00212 CH$LINK: NIKKAJI J4.501B CH$LINK: PUBCHEM SID:3512 AC$INSTRUMENT: Qstar, Applied Biosystems AC$INSTRUMENT_TYPE: LC-ESI-QTOF AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE MS$FOCUSED_ION: PRECURSOR_M/Z 266 MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- PK$ANNOTATION: 107.0357711171 134.0466701544 136.0623202186 266.0889288996 PK$NUM_PEAK: N/A PK$PEAK: m/z int. rel.int. N/A ', 'ACCESSION: FU000001 RECORD_TITLE: 3-Man2GlcNAc; LC-ESI-QQ; MS2; CE:15V; Amide DATE: 2016.01.19 (Created 2009.02.18, modified 2011.05.06) AUTHORS: Matsuura F, Ohta M, Kittaka M, Faculty of Life Science and Biotechnology, Fukuyama University LICENSE: CC BY-SA CH$NAME: 3-Man2GlcNAc CH$NAME: Man-alpha-1-3Man-beta-1-4GlcNac CH$COMPOUND_CLASS: Natural Product; Oligosaccharide; N-linked glycan; High-mannose type CH$FORMULA: C20H35NO16 CH$EXACT_MASS: 545.19558 CH$SMILES: CC(=O)NC(C(O)1)C(O)C(OC(O2)C(O)C(OC(O3)C(O)C(O)C(O)C(CO)3)C(O)C(CO)2)C(CO)O1 CH$IUPAC: InChI=1/C20H35NO16/c1-5(25)21-9-12(28)16(8(4-24)33-18(9)32)36-20-15(31)17(11(27)7(3-23)35-20)37-19-14(30)13(29)10(26)6(2-22)34-19/h6-20,22-24,26-32H,2-4H2,1H3,(H,21,25)/t6-,7-,8-,9-,10-,11-,12-,13+,14-,15+,16-,17+,18+,19-,20+/m1/s1/f/h21H CH$LINK: CHEMSPIDER 24606097 CH$LINK: KEGG G00319 CH$LINK: OligosaccharideDataBase man 547428 CH$LINK: OligosaccharideDataBase2D map5 ODS=1.21 Amide=2.85 AC$INSTRUMENT: 2695 HPLC Quadro Micro API, Waters AC$INSTRUMENT_TYPE: LC-ESI-QQ AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE POSITIVE AC$MASS_SPECTROMETRY: COLLISION_ENERGY 15.0 V AC$MASS_SPECTROMETRY: DATAFORMAT Centroid AC$MASS_SPECTROMETRY: DESOLVATION_GAS_FLOW 897 L/Hr AC$MASS_SPECTROMETRY: DESOLVATION_TEMPERATURE 399 C AC$MASS_SPECTROMETRY: FRAGMENTATION_METHOD LOW-ENERGY CID AC$MASS_SPECTROMETRY: IONIZATION ESI AC$MASS_SPECTROMETRY: SCANNING 1 amu/sec (m/z = 20-2040) AC$MASS_SPECTROMETRY: SOURCE_TEMPERATURE 100C AC$CHROMATOGRAPHY: COLUMN_NAME TSK-GEL Amide-80 2.0 mm X 250 mm (TOSOH) AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C AC$CHROMATOGRAPHY: FLOW_GRADIENT 74/26 at 0 min, 50/50 at 60 min. AC$CHROMATOGRAPHY: FLOW_RATE 0.2 ml/min AC$CHROMATOGRAPHY: RETENTION_TIME 7.080 min AC$CHROMATOGRAPHY: SAMPLING_CONE 43.10 V AC$CHROMATOGRAPHY: SOLVENT CH3CN/H2O MS$FOCUSED_ION: DERIVATIVE_FORM C29H46N2O17 MS$FOCUSED_ION: DERIVATIVE_MASS 694.27965 MS$FOCUSED_ION: DERIVATIVE_TYPE ABEE (p-Aminobenzoic acid ethyl ester) MS$FOCUSED_ION: PRECURSOR_M/Z 695.00 MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+ PK$SPLASH: splash10-00080az000-bfe86aa7211a87812a06 PK$NUM_PEAK: 8 PK$PEAK: m/z int. rel.int. 370.8 3.277e5 366 371.4 3.036e4 34 532.0 5.812e4 65 532.6 2.982e5 333 533.3 5.196e4 58 694.1 4.564e5 510 694.8 8.939e5 999 695.4 5.537e4 62 ', 'ACCESSION: FU000002 RECORD_TITLE: 3-Man2GlcNAc; LC-ESI-QQ; MS2; CE:20V; Amide DATE: 2016.01.19 (Created 2009.02.18, modified 2011.05.06) AUTHORS: Matsuura F, Ohta M, Kittaka M, Faculty of Life Science and Biotechnology, Fukuyama University LICENSE: CC BY-SA CH$NAME: 3-Man2GlcNAc CH$NAME: Man-alpha-1-3Man-beta-1-5GlcNac CH$COMPOUND_CLASS: Natural Product; Oligosaccharide; N-linked glycan; High-mannose type CH$FORMULA: C20H35NO16 CH$EXACT_MASS: 545.19558 CH$SMILES: CC(=O)NC(C(O)1)C(O)C(OC(O2)C(O)C(OC(O3)C(O)C(O)C(O)C(CO)3)C(O)C(CO)2)C(CO)O1 CH$IUPAC: InChI=1/C20H35NO16/c1-5(25)21-9-12(28)16(8(4-24)33-18(9)32)36-20-15(31)17(11(27)7(3-23)35-20)37-19-14(30)13(29)10(26)6(2-22)34-19/h6-20,22-24,26-32H,2-4H2,1H3,(H,21,25)/t6-,7-,8-,9-,10-,11-,12-,13+,14-,15+,16-,17+,18+,19-,20+/m1/s1/f/h21H CH$LINK: CHEMSPIDER 24606097 CH$LINK: KEGG G00319 CH$LINK: OligosaccharideDataBase man 547428 CH$LINK: OligosaccharideDataBase2D map5 ODS=1.21 Amide=2.85 AC$INSTRUMENT: 2695 HPLC Quadro Micro API, Waters AC$INSTRUMENT_TYPE: LC-ESI-QQ AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE POSITIVE AC$MASS_SPECTROMETRY: COLLISION_ENERGY 20.0 V AC$MASS_SPECTROMETRY: DATAFORMAT Centroid AC$MASS_SPECTROMETRY: DESOLVATION_GAS_FLOW 897 L/Hr AC$MASS_SPECTROMETRY: DESOLVATION_TEMPERATURE 399 C AC$MASS_SPECTROMETRY: FRAGMENTATION_METHOD LOW-ENERGY CID AC$MASS_SPECTROMETRY: IONIZATION ESI AC$MASS_SPECTROMETRY: SCANNING 1 amu/sec (m/z = 20-2040) AC$MASS_SPECTROMETRY: SOURCE_TEMPERATURE 100C AC$CHROMATOGRAPHY: COLUMN_NAME TSK-GEL Amide-80 2.0 mm X 250 mm (TOSOH) AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C AC$CHROMATOGRAPHY: FLOW_GRADIENT 74/26 at 0 min, 50/50 at 60 min. AC$CHROMATOGRAPHY: FLOW_RATE 0.2 ml/min AC$CHROMATOGRAPHY: RETENTION_TIME 7.088 min AC$CHROMATOGRAPHY: SAMPLING_CONE 43.10 V AC$CHROMATOGRAPHY: SOLVENT CH3CN/H2O MS$FOCUSED_ION: DERIVATIVE_FORM C29H46N2O17 MS$FOCUSED_ION: DERIVATIVE_MASS 694.27965 MS$FOCUSED_ION: DERIVATIVE_TYPE ABEE (p-Aminobenzoic acid ethyl ester) MS$FOCUSED_ION: PRECURSOR_M/Z 695.00 MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+ PK$SPLASH: splash10-000z0fb000-52e2618a90c53226e008 PK$NUM_PEAK: 10 PK$PEAK: m/z int. rel.int. 324.9 5.549e4 65 370.8 8.511e5 999 371.3 8.989e4 106 486.8 2.622e4 31 532.0 5.832e4 68 532.7 3.515e5 413 533.3 3.910e4 46 693.9 4.249e4 50 694.5 1.979e5 232 695.3 9.682e4 114 ', 'ACCESSION: TY000040 RECORD_TITLE: Aconitine; LC-ESI-ITTOF; MS; [M+H]+ DATE: 2016.01.19 (Created 2008.10.10, modified 2011.05.06) AUTHORS: Ken Tanaka LICENSE: CC BY-SA CH$NAME: Aconitine CH$NAME: NSC56464 CH$NAME: 16-Ethyl-1alpha,6alpha,19beta-trimethoxy-4-(methoxymethyl)-aconitane-3alpha,8,10alpha,11,18alpha-pentol, 8-acetate 10-benzoate CH$NAME: 20-ethyl-3alpha,13,15alpha-trihydroxy-1alpha,6alpha,16beta-trimethoxy-4-(methoxymethyl)aconitane-8,14alpha-diyl 8-acetate 14-benzoate CH$COMPOUND_CLASS: Natural Product; Alkaloid CH$FORMULA: C34H47NO11 CH$EXACT_MASS: 645.31491 CH$SMILES: COC(C7)C(C61[H])(C5([H])2)C(N(CC(COC)6C7O)CC)([H])C(C(C5([H])3)(C(C(OC)C(O)(C(OC(=O)c(c4)cccc4)3)C2)O)OC(C)=O)([H])C1OC CH$IUPAC: InChI=1S/C34H47NO11/c1-7-35-15-31(16-41-3)20(37)13-21(42-4)33-19-14-32(40)28(45-30(39)18-11-9-8-10-12-18)22(19)34(46-17(2)36,27(38)29(32)44-6)23(26(33)35)24(43-5)25(31)33/h8-12,19-29,37-38,40H,7,13-16H2,1-6H3/t19-,20-,21+,22-,23+,24+,25-,26+,27+,28-,29+,31+,32-,33+,34-/m1/s1 CH$LINK: CAS 302-27-2 CH$LINK: NIKKAJI J9.871J CH$LINK: PUBCHEM 245005 AC$INSTRUMENT: Shimadzu LC20A-IT-TOFMS AC$INSTRUMENT_TYPE: LC-ESI-ITTOF AC$MASS_SPECTROMETRY: MS_TYPE MS AC$MASS_SPECTROMETRY: ION_MODE POSITIVE AC$MASS_SPECTROMETRY: CDL_TEMPERATURE 200 C AC$MASS_SPECTROMETRY: INTERFACE_VOLTAGE +4.50 kV AC$MASS_SPECTROMETRY: SCANNING_RANGE 100-2000 AC$CHROMATOGRAPHY: COLUMN_NAME Waters Atlantis T3 (2.1 x 150 mm, 5 um) AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C AC$CHROMATOGRAPHY: FLOW_GRADIENT 10 % B to 100 % B/40 min AC$CHROMATOGRAPHY: FLOW_RATE 0.2 ml/min AC$CHROMATOGRAPHY: RETENTION_TIME 1197.701 AC$CHROMATOGRAPHY: SOLVENT (A)5 mM ammonium acetate, (B)CH3CN MS$FOCUSED_ION: ION_TYPE [M+H]+ PK$SPLASH: splash10-000000z000-1f6554288e1249b37bcb PK$NUM_PEAK: 3 PK$PEAK: m/z int. rel.int. 646.3223 64380108 999 647.3252 26819201 416 648.3309 7305831 113 ', 'ACCESSION: TY000041 RECORD_TITLE: Atropine; LC-ESI-ITTOF; MS; [M+H]+ DATE: 2016.01.19 (Created 2008.10.10, modified 2011.05.06) AUTHORS: Ken Tanaka LICENSE: CC BY-SA CH$NAME: Atropine CH$NAME: Benzeneacetic acid, alpha-(hydroxymethyl)- (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl ester CH$NAME: 1alphaH,5alphaH-Tropan-3alpha-ol (+-)-tropate (ester) CH$NAME: Benzeneacetic acid, alpha-(hydroxymethyl)-, 8-methyl-8-azabicyclo[3.2.1]oct-3-yl ester, endo- CH$NAME: (+-)-Atropine CH$NAME: (+-)-Hyoscyamine CH$NAME: Tropine (+-)-tropate CH$NAME: dl-Tropyl tropate CH$NAME: dl-Hyoscyamine CH$NAME: Tropine tropate CH$NAME: Atropinol CH$NAME: Eyesules CH$NAME: Atropen CH$NAME: Isopto-atropine CH$NAME: Troyl tropate CH$NAME: Belladenal CH$NAME: Atropina CH$NAME: Cytospaz CH$NAME: Donnagel CH$NAME: Anaspaz CH$NAME: Atnaa CH$NAME: Lonox CH$NAME: Neo-Diophen CH$NAME: DL-Tropanyl 2-hydroxy-1-phenylpropionate CH$NAME: 2-Phenylhydracrylic acid 3-alpha-tropanyl ester CH$NAME: tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate CH$NAME: 8-Methyl-8-azabicyclo[3.2.1]oct-3-yl tropate CH$NAME: 8-Methyl-8-azabicyclo[3.2.1]oct-3-yl 3-hydroxy-2-phenylpropanoate CH$NAME: alpha-(Hydroxymethyl)benzeneacetic acid 8-methyl-8-azabicyclo(3.2.1)oct-3-yl ester CH$NAME: Benzeneacetic acid, alpha-(hydroxymethyl)-, (3-endo)-8-methyl-8-azabicyclo(3.2.1)oct-3-yl ester CH$NAME: (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl (2S)-3-hydroxy-2-phenylpropanoate CH$NAME: [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] 3-hydroxy-2-phenylpropanoate CH$NAME: beta-(Hydroxymethyl)benzeneacetic acid 8-methyl-8-azabicyclo[3.2.1]oct-3-yl ester CH$NAME: endo-(+/-)-alpha-(Hydroxymethyl)benzeneacetic acid 8-methyl-8-azabicyclo[3.2.1]oct-3-yl ester CH$COMPOUND_CLASS: Natural Product; Alkaloid CH$FORMULA: C17H23NO3 CH$EXACT_MASS: 289.16779 CH$SMILES: OCC(C(=O)OC(C2)CC(C3)N(C)C(C3)2)c(c1)cccc1 CH$IUPAC: InChI=1S/C17H23NO3/c1-18-13-7-8-14(18)10-15(9-13)21-17(20)16(11-19)12-5-3-2-4-6-12/h2-6,13-16,19H,7-11H2,1H3/t13-,14+,15+,16? CH$LINK: CAS 51-55-8 CH$LINK: NIKKAJI J237.402A CH$LINK: PUBCHEM 174174 AC$INSTRUMENT: Shimadzu LC20A-IT-TOFMS AC$INSTRUMENT_TYPE: LC-ESI-ITTOF AC$MASS_SPECTROMETRY: MS_TYPE MS AC$MASS_SPECTROMETRY: ION_MODE POSITIVE AC$MASS_SPECTROMETRY: CDL_TEMPERATURE 200 C AC$MASS_SPECTROMETRY: INTERFACE_VOLTAGE +4.50 kV AC$MASS_SPECTROMETRY: SCANNING_RANGE 100-2000 AC$CHROMATOGRAPHY: COLUMN_NAME Waters Atlantis T3 (2.1 x 150 mm, 5 um) AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C AC$CHROMATOGRAPHY: FLOW_GRADIENT 10 % B to 100 % B/40 min AC$CHROMATOGRAPHY: FLOW_RATE 0.2 ml/min AC$CHROMATOGRAPHY: RETENTION_TIME 641.701 AC$CHROMATOGRAPHY: SOLVENT (A)5 mM ammonium acetate, (B)CH3CN MS$FOCUSED_ION: ION_TYPE [M+H]+ PK$SPLASH: splash10-00z0000000-bdadd43ab0e2444986f1 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 290.1754 109188681 999 291.1762 21571851 197 ' ], ## end results 'Method \'get_massbank_records_by_chunk\' works with a full ids list and return a nice and unique list of records from WS-MassBank'); #### #### ##### ###### ################################################ ###### ##### ##### ###### ###### ## END of MAPPER SEQUENCE ## #### #### ##### ###### ################################################ ###### ##### ##### ###### ###### } #### #### ##### ###### ################################################ ###### ##### ##### ###### ###### ## START of API SEQUENCE ## #### #### ##### ###### ################################################ ###### ##### ##### ###### ###### elsif ($sequence eq "API") { ## testing connectMassBank on Japan and DE servers. ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n\t\t\t\t * * * * * * \n" ; print "\t * * * - - - Test MassBank API from SOAP - - - * * * \n\n" ; ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test connectMassBankJP with real uri and proxy **\n" ; $current_test++; isa_ok( connectMassBankJPTest(), 'SOAP::Lite' ); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test connectMassBankDE with real uri and proxy **\n" ; $current_test++ ; isa_ok( connectMassBankDETest(), 'SOAP::Lite' ); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getInstrumentTypes with the JP server **\n" ; $current_test++ ; #is_deeply( getInstrumentTypesTest('JP'), ['APCI-ITFT', 'APCI-ITTOF','CE-ESI-TOF', 'CI-B', 'EI-B', 'EI-EBEB', 'ESI-ITFT', 'ESI-ITTOF', 'FAB-B', 'FAB-EB', 'FAB-EBEB', 'FD-B', 'FI-B', 'GC-EI-QQ', 'GC-EI-TOF', 'LC-APCI-QTOF', 'LC-APPI-QQ', 'LC-ESI-IT', 'LC-ESI-ITFT', 'LC-ESI-ITTOF', 'LC-ESI-Q', 'LC-ESI-QFT', 'LC-ESI-QIT', 'LC-ESI-QQ', 'LC-ESI-QTOF', 'LC-ESI-TOF', 'MALDI-QIT', 'MALDI-TOF', 'MALDI-TOFTOF'], "Works with \'JP server\' and return a list of instrument types"); print "-- no test -- skipped because JP getInstrumentTypes method is down\n" ; print "\n** Test $current_test getInstrumentTypes with the DE server **\n" ; $current_test++ ; #is_deeply( getInstrumentTypesTest('EU'), ['APCI-ITFT', 'APCI-ITTOF', 'CE-ESI-TOF', 'CI-B', 'EI-B', 'EI-EBEB', 'ESI-FTICR', 'ESI-ITFT', 'ESI-ITTOF', 'FAB-B', 'FAB-EB', 'FAB-EBEB', 'FD-B', 'FI-B', 'GC-EI-QQ', 'GC-EI-TOF', 'HPLC-ESI-TOF', 'LC-APCI-Q', 'LC-APCI-QTOF', 'LC-APPI-QQ', 'LC-ESI-IT', 'LC-ESI-ITFT', 'LC-ESI-ITTOF', 'LC-ESI-Q', 'LC-ESI-QFT', 'LC-ESI-QIT', 'LC-ESI-QQ', 'LC-ESI-QTOF', 'LC-ESI-TOF', 'MALDI-QIT', 'MALDI-TOF', 'MALDI-TOFTOF', 'UPLC-ESI-QTOF'], "Works with $server server and return a list of instrument types"); print "-- no test -- skipped because DE method is down\n" ; ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test initRecordObject on a well formatted massbank record string **\n" ; $current_test++ ; is_deeply( initRecordObjectTest('ACCESSION: KOX00001 RECORD_TITLE: GABA; LC-ESI-QTOF; MS2; MERGED; [M-H]- DATE: 2011.08.24 (Created 2008.11.28) AUTHORS: Institute for Advanced Biosciences, Keio Univ. LICENSE: Copyright 2006-2011 Keio COMMENT: Peak data in the following records are not open to the public as requested by their authors. COMMENT: Instead MassBank provides the merged spectra for the public. COMMENT: This record was generated by merging the following three MassBank records. COMMENT: [Merging] KO004290 GABA; LC-ESI-QTOF; MS2; CE:10 V [M-H]- COMMENT: [Merging] KO004291 GABA; LC-ESI-QTOF; MS2; CE:20 V [M-H]- COMMENT: [Merging] KO004292 GABA; LC-ESI-QTOF; MS2; CE:30 V [M-H]- CH$NAME: GABA CH$NAME: 4-Aminobutanoate CH$NAME: 4-Aminobutanoic acid CH$NAME: 4-Aminobutylate CH$NAME: 4-Aminobutyrate CH$NAME: 4-Aminobutyric acid CH$NAME: gamma-Aminobutyric acid CH$COMPOUND_CLASS: N/A CH$FORMULA: C4H9NO2 CH$EXACT_MASS: 103.06333 CH$SMILES: NCCCC(O)=O CH$IUPAC: InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) CH$LINK: CAS 56-12-2 CH$LINK: CHEBI 30566 CH$LINK: KEGG C00334 CH$LINK: NIKKAJI J1.375G CH$LINK: PUBCHEM SID:3628 AC$INSTRUMENT: Qstar, Applied Biosystems AC$INSTRUMENT_TYPE: LC-ESI-QTOF AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE MS$FOCUSED_ION: PRECURSOR_M/Z 102 MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- PK$ANNOTATION: 41.9979886273 84.0449388199 102.0555035062 PK$NUM_PEAK: N/A PK$PEAK: m/z int. rel.int. N/A '), { 'CH$NAME' => 'gamma-Aminobutyric acid', 'AC$MASS_SPECTROMETRY' => 'ION_MODE NEGATIVE', 'CH$LINK: PUBCHEM SID' => '3628', 'ACCESSION' => 'KOX00001', 'CH$COMPOUND_CLASS' => 'N/A', 'LICENSE' => 'Copyright 2006-2011 Keio', 'COMMENT: [Merging] KO004292 GABA; LC-ESI-QTOF; MS2; CE' => '30 V [M-H]-', 'COMMENT: [Merging] KO004291 GABA; LC-ESI-QTOF; MS2; CE' => '20 V [M-H]-', 'CH$IUPAC' => 'InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7)', 'PK$ANNOTATION' => '41.9979886273 84.0449388199 102.0555035062', 'AUTHORS' => 'Institute for Advanced Biosciences, Keio Univ.', 'PK$NUM_PEAK' => 'N/A', 'CH$SMILES' => 'NCCCC(O)=O', 'AC$INSTRUMENT_TYPE' => 'LC-ESI-QTOF', 'CH$EXACT_MASS' => '103.06333', 'CH$LINK' => 'NIKKAJI J1.375G', 'CH$FORMULA' => 'C4H9NO2', 'PK$PEAK' => { 'relint' => [], 'int' => [], 'mz' => [] }, 'DATE' => '2011.08.24 (Created 2008.11.28)', 'MS$FOCUSED_ION' => 'PRECURSOR_TYPE [M-H]-', 'RECORD_TITLE' => 'GABA; LC-ESI-QTOF; MS2; MERGED; [M-H]-', 'COMMENT: [Merging] KO004290 GABA; LC-ESI-QTOF; MS2; CE' => '10 V [M-H]-', 'AC$INSTRUMENT' => 'Qstar, Applied Biosystems', 'COMMENT' => 'This record was generated by merging the following three MassBank records.' }, "Works with a well formatted massbank record string and return one record object from \"KOX00001\" id"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test initRecordObject on a well formatted massbank record string (has peaks !!) **\n" ; $current_test++ ; is_deeply( initRecordObjectTest('ACCESSION: TY000040 RECORD_TITLE: Aconitine; LC-ESI-ITTOF; MS; [M+H]+ DATE: 2011.05.06 (Created 2008.10.10) AUTHORS: Ken Tanaka LICENSE: CC BY-SA CH$NAME: Aconitine CH$NAME: NSC56464 CH$NAME: 16-Ethyl-1alpha,6alpha,19beta-trimethoxy-4-(methoxymethyl)-aconitane-3alpha,8,10alpha,11,18alpha-pentol, 8-acetate 10-benzoate CH$NAME: 20-ethyl-3alpha,13,15alpha-trihydroxy-1alpha,6alpha,16beta-trimethoxy-4-(methoxymethyl)aconitane-8,14alpha-diyl 8-acetate 14-benzoate CH$COMPOUND_CLASS: Natural Product; Alkaloid CH$FORMULA: C34H47NO11 CH$EXACT_MASS: 645.31491 CH$SMILES: COC(C7)C(C61[H])(C5([H])2)C(N(CC(COC)6C7O)CC)([H])C(C(C5([H])3)(C(C(OC)C(O)(C(OC(=O)c(c4)cccc4)3)C2)O)OC(C)=O)([H])C1OC CH$IUPAC: InChI=1S/C34H47NO11/c1-7-35-15-31(16-41-3)20(37)13-21(42-4)33-19-14-32(40)28(45-30(39)18-11-9-8-10-12-18)22(19)34(46-17(2)36,27(38)29(32)44-6)23(26(33)35)24(43-5)25(31)33/h8-12,19-29,37-38,40H,7,13-16H2,1-6H3/t19-,20-,21+,22-,23+,24+,25-,26+,27+,28-,29+,31+,32-,33+,34-/m1/s1 CH$LINK: CAS 302-27-2 CH$LINK: NIKKAJI J9.871J CH$LINK: PUBCHEM 245005 AC$INSTRUMENT: Shimadzu LC20A-IT-TOFMS AC$INSTRUMENT_TYPE: LC-ESI-ITTOF AC$MASS_SPECTROMETRY: MS_TYPE MS AC$MASS_SPECTROMETRY: ION_MODE POSITIVE AC$MASS_SPECTROMETRY: CDL_TEMPERATURE 200 C AC$MASS_SPECTROMETRY: INTERFACE_VOLTAGE +4.50 kV AC$MASS_SPECTROMETRY: SCANNING_RANGE 100-2000 AC$CHROMATOGRAPHY: COLUMN_NAME Waters Atlantis T3 (2.1 x 150 mm, 5 um) AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C AC$CHROMATOGRAPHY: FLOW_GRADIENT 10 % B to 100 % B/40 min AC$CHROMATOGRAPHY: FLOW_RATE 0.2 ml/min AC$CHROMATOGRAPHY: RETENTION_TIME 1197.701 AC$CHROMATOGRAPHY: SOLVENT (A)5 mM ammonium acetate, (B)CH3CN MS$FOCUSED_ION: ION_TYPE [M+H]+ PK$NUM_PEAK: 3 PK$PEAK: m/z int. rel.int. 646.3223 64380108 999 647.3252 26819201 416 648.3309 7305831 113 '), { 'MS$FOCUSED_ION' => 'ION_TYPE [M+H]+', 'CH$COMPOUND_CLASS' => 'Natural Product; Alkaloid', 'CH$EXACT_MASS' => '645.31491', 'AC$MASS_SPECTROMETRY' => 'SCANNING_RANGE 100-2000', 'AC$INSTRUMENT' => 'Shimadzu LC20A-IT-TOFMS', 'PK$PEAK' => { 'mz' => [ '646.3223', '647.3252', '648.3309' ], 'int' => [ '64380108', '26819201', '7305831' ], 'relint' => [ '999', '416', '113' ] }, 'CH$IUPAC' => 'InChI=1S/C34H47NO11/c1-7-35-15-31(16-41-3)20(37)13-21(42-4)33-19-14-32(40)28(45-30(39)18-11-9-8-10-12-18)22(19)34(46-17(2)36,27(38)29(32)44-6)23(26(33)35)24(43-5)25(31)33/h8-12,19-29,37-38,40H,7,13-16H2,1-6H3/t19-,20-,21+,22-,23+,24+,25-,26+,27+,28-,29+,31+,32-,33+,34-/m1/s1', 'AC$CHROMATOGRAPHY' => 'SOLVENT (A)5 mM ammonium acetate, (B)CH3CN', 'DATE' => '2011.05.06 (Created 2008.10.10)', 'LICENSE' => 'CC BY-SA', 'AC$INSTRUMENT_TYPE' => 'LC-ESI-ITTOF', 'CH$FORMULA' => 'C34H47NO11', 'CH$LINK' => 'PUBCHEM 245005', 'CH$NAME' => '20-ethyl-3alpha,13,15alpha-trihydroxy-1alpha,6alpha,16beta-trimethoxy-4-(methoxymethyl)aconitane-8,14alpha-diyl 8-acetate 14-benzoate', 'PK$NUM_PEAK' => '3', 'ACCESSION' => 'TY000040', 'RECORD_TITLE' => 'Aconitine; LC-ESI-ITTOF; MS; [M+H]+', 'CH$SMILES' => 'COC(C7)C(C61[H])(C5([H])2)C(N(CC(COC)6C7O)CC)([H])C(C(C5([H])3)(C(C(OC)C(O)(C(OC(=O)c(c4)cccc4)3)C2)O)OC(C)=O)([H])C1OC', 'AUTHORS' => 'Ken Tanaka' }, "Works with a well formatted massbank record string and return one record object from \"KOX00001\" id"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getRecord on $server server with a true ID **\n" ; $current_test++ ; is_deeply( getRecordInfoTest($server, ['KOX00001']), ['ACCESSION: KOX00001 RECORD_TITLE: GABA; LC-ESI-QTOF; MS2; MERGED; [M-H]- DATE: 2011.08.24 (Created 2008.11.28) AUTHORS: Institute for Advanced Biosciences, Keio Univ. LICENSE: Copyright 2006-2011 Keio COMMENT: Peak data in the following records are not open to the public as requested by their authors. COMMENT: Instead MassBank provides the merged spectra for the public. COMMENT: This record was generated by merging the following three MassBank records. COMMENT: [Merging] KO004290 GABA; LC-ESI-QTOF; MS2; CE:10 V [M-H]- COMMENT: [Merging] KO004291 GABA; LC-ESI-QTOF; MS2; CE:20 V [M-H]- COMMENT: [Merging] KO004292 GABA; LC-ESI-QTOF; MS2; CE:30 V [M-H]- CH$NAME: GABA CH$NAME: 4-Aminobutanoate CH$NAME: 4-Aminobutanoic acid CH$NAME: 4-Aminobutylate CH$NAME: 4-Aminobutyrate CH$NAME: 4-Aminobutyric acid CH$NAME: gamma-Aminobutyric acid CH$COMPOUND_CLASS: N/A CH$FORMULA: C4H9NO2 CH$EXACT_MASS: 103.06333 CH$SMILES: NCCCC(O)=O CH$IUPAC: InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) CH$LINK: CAS 56-12-2 CH$LINK: CHEBI 30566 CH$LINK: KEGG C00334 CH$LINK: NIKKAJI J1.375G CH$LINK: PUBCHEM SID:3628 AC$INSTRUMENT: Qstar, Applied Biosystems AC$INSTRUMENT_TYPE: LC-ESI-QTOF AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE MS$FOCUSED_ION: PRECURSOR_M/Z 102 MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- PK$ANNOTATION: 41.9979886273 84.0449388199 102.0555035062 PK$NUM_PEAK: N/A PK$PEAK: m/z int. rel.int. N/A '], "Works with $server server and return one record from \"KOX00001\" id"); ## test a false massbank ID - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getRecord with a false ID **\n" ; $current_test++ ; is_deeply( getRecordInfoTest($server, ['KOX100101']), [undef], "Method \'getRecordInfo\' works with $server server and manage no sended record from \"KOX100101\" a false id"); ## test a false massbank ID - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getRecord with a false ID into a real list **\n" ; $current_test++; is_deeply( getRecordInfoTest($server, ['KOX100101', 'KOX00001']), ['ACCESSION: KOX00001 RECORD_TITLE: GABA; LC-ESI-QTOF; MS2; MERGED; [M-H]- DATE: 2011.08.24 (Created 2008.11.28) AUTHORS: Institute for Advanced Biosciences, Keio Univ. LICENSE: Copyright 2006-2011 Keio COMMENT: Peak data in the following records are not open to the public as requested by their authors. COMMENT: Instead MassBank provides the merged spectra for the public. COMMENT: This record was generated by merging the following three MassBank records. COMMENT: [Merging] KO004290 GABA; LC-ESI-QTOF; MS2; CE:10 V [M-H]- COMMENT: [Merging] KO004291 GABA; LC-ESI-QTOF; MS2; CE:20 V [M-H]- COMMENT: [Merging] KO004292 GABA; LC-ESI-QTOF; MS2; CE:30 V [M-H]- CH$NAME: GABA CH$NAME: 4-Aminobutanoate CH$NAME: 4-Aminobutanoic acid CH$NAME: 4-Aminobutylate CH$NAME: 4-Aminobutyrate CH$NAME: 4-Aminobutyric acid CH$NAME: gamma-Aminobutyric acid CH$COMPOUND_CLASS: N/A CH$FORMULA: C4H9NO2 CH$EXACT_MASS: 103.06333 CH$SMILES: NCCCC(O)=O CH$IUPAC: InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) CH$LINK: CAS 56-12-2 CH$LINK: CHEBI 30566 CH$LINK: KEGG C00334 CH$LINK: NIKKAJI J1.375G CH$LINK: PUBCHEM SID:3628 AC$INSTRUMENT: Qstar, Applied Biosystems AC$INSTRUMENT_TYPE: LC-ESI-QTOF AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE MS$FOCUSED_ION: PRECURSOR_M/Z 102 MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- PK$ANNOTATION: 41.9979886273 84.0449388199 102.0555035062 PK$NUM_PEAK: N/A PK$PEAK: m/z int. rel.int. N/A '], "Method \'getRecordInfo\' works with $server server and don\'t send record from \"KOX100101\" a false id into a list"); ## test an undef massbank IDs list - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getRecord with a undef list of IDs **\n" ; $current_test++; is_deeply( getRecordInfoTest($server, undef), [], "Method \'getRecordInfo\' works with $server server and manage undef massbank ids list"); ## test an empty massbank IDs list - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getRecord with a void list of IDs **\n" ; $current_test++ ; is_deeply( getRecordInfoTest($server, [] ), [], "Method \'getRecordInfo\' works with $server server and manage empty massbank ids list"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - print "\n** Test $current_test getRecord on $server server with only one real ID **\n" ; $current_test++; is_deeply( getRecordInfoTest($server, ['KOX00001']), ['ACCESSION: KOX00001 RECORD_TITLE: GABA; LC-ESI-QTOF; MS2; MERGED; [M-H]- DATE: 2011.08.24 (Created 2008.11.28) AUTHORS: Institute for Advanced Biosciences, Keio Univ. LICENSE: Copyright 2006-2011 Keio COMMENT: Peak data in the following records are not open to the public as requested by their authors. COMMENT: Instead MassBank provides the merged spectra for the public. COMMENT: This record was generated by merging the following three MassBank records. COMMENT: [Merging] KO004290 GABA; LC-ESI-QTOF; MS2; CE:10 V [M-H]- COMMENT: [Merging] KO004291 GABA; LC-ESI-QTOF; MS2; CE:20 V [M-H]- COMMENT: [Merging] KO004292 GABA; LC-ESI-QTOF; MS2; CE:30 V [M-H]- CH$NAME: GABA CH$NAME: 4-Aminobutanoate CH$NAME: 4-Aminobutanoic acid CH$NAME: 4-Aminobutylate CH$NAME: 4-Aminobutyrate CH$NAME: 4-Aminobutyric acid CH$NAME: gamma-Aminobutyric acid CH$COMPOUND_CLASS: N/A CH$FORMULA: C4H9NO2 CH$EXACT_MASS: 103.06333 CH$SMILES: NCCCC(O)=O CH$IUPAC: InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) CH$LINK: CAS 56-12-2 CH$LINK: CHEBI 30566 CH$LINK: KEGG C00334 CH$LINK: NIKKAJI J1.375G CH$LINK: PUBCHEM SID:3628 AC$INSTRUMENT: Qstar, Applied Biosystems AC$INSTRUMENT_TYPE: LC-ESI-QTOF AC$MASS_SPECTROMETRY: MS_TYPE MS2 AC$MASS_SPECTROMETRY: ION_MODE NEGATIVE MS$FOCUSED_ION: PRECURSOR_M/Z 102 MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- PK$ANNOTATION: 41.9979886273 84.0449388199 102.0555035062 PK$NUM_PEAK: N/A PK$PEAK: m/z int. rel.int. N/A '], "Method \'getRecordInfo\' works with $server server and return one record from \"KOX00001\" id"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff # Structure of res : %ret = {'res' => [], 'num_res' => int, 'pcgroup_id'=> int } print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and real search parameters **\n" ; $current_test++; is_deeply( searchSpectrumTest( ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['300', '300', '300', '300', '300', '300', '300'], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), { 'num_res' => 2, 'pcgroup_id' => 1, 'res' => [ { 'title' => 'Lormetazepam; LC-ESI-Q; MS; POS; 60 V', 'exactMass' => '334.02758', 'score' => '0.428034082411', 'id' => 'WA001260', 'formula' => 'C16H12Cl2N2O2' }, { 'formula' => 'C16H12Cl2N2O2', 'exactMass' => '334.02758', 'score' => '0.385859601865', 'id' => 'WA001261', 'title' => 'Lormetazepam; LC-ESI-Q; MS; POS; 45 V' } ] }, "Method \'searchSpectrum\' works with $server server and return a list of entries from given mzs list"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff # Structure of res : %ret = {'res' => [], 'num_res' => int, 'pcgroup_id'=> int } print "\n** Test $current_test searchSpectrum with the Atrazine fingerprint and real search parameters **\n" ; $current_test++; is_deeply( searchSpectrumTest( ['68.0245', '96.056', '104.0014', '132.0328', '138.1031', '146.0233', '174.0547', '180.125', '188.0703'], ['300', '300', '300', '300', '300', '300', '300'], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), { 'num_res' => 2, 'pcgroup_id' => 1, 'res' => [ { 'title' => 'Lormetazepam; LC-ESI-Q; MS; POS; 60 V', 'exactMass' => '334.02758', 'score' => '0.428034082411', 'id' => 'WA001260', 'formula' => 'C16H12Cl2N2O2' }, { 'formula' => 'C16H12Cl2N2O2', 'exactMass' => '334.02758', 'score' => '0.385859601865', 'id' => 'WA001261', 'title' => 'Lormetazepam; LC-ESI-Q; MS; POS; 45 V' } ] }, "Method \'searchSpectrum\' works with $server server and return the Atrazine record from given mzs list"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and real search parameters **\n" ; $current_test++; is_deeply( searchSpectrumTest( ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['5', '5', '5', '5', '5', '5', '5'], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), { 'num_res' => 2, 'pcgroup_id' => 1, 'res' => [ { 'title' => 'Lormetazepam; LC-ESI-Q; MS; POS; 60 V', 'exactMass' => '334.02758', 'score' => '0.428034082411', 'id' => 'WA001260', 'formula' => 'C16H12Cl2N2O2' }, { 'formula' => 'C16H12Cl2N2O2', 'exactMass' => '334.02758', 'score' => '0.385859601865', 'id' => 'WA001261', 'title' => 'Lormetazepam; LC-ESI-Q; MS; POS; 45 V' } ] }, "Method \'searchSpectrum\' works with $server server and return a list of entries from given mzs list with no intensity (very low in true)"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and real search parameters - /!\\ Bug - Real intensity **\n" ; $current_test++; is_deeply( searchSpectrumTest( ['121.5145853','121.6260795','126.186473','126.2979602','126.4094198','184.0731041'], ['614328.101','298110.8522','1372105.065','799423.8448','99064.65118','2342541.316'], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), { 'num_res' => 1, 'pcgroup_id' => 1, 'res' => [ { 'formula' => 'C12H13NO2', 'id' => 'KO003209', 'title' => '3-Indolebutyric acid; LC-ESI-QQ; MS2; CE:30 V; [M+H]+', 'score' => '0.239887404489', 'exactMass' => '203.09463' } ] }, "Method \'searchSpectrum\' works with $server server and return a list of entries from given mzs list /!\\ Bug - Real intensity"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and real search parameters - /!\\ Bug - Real relative intensity **\n" ; $current_test++; is_deeply( searchSpectrumTest( ['121.51459','121.62608','126.18647','126.29796','126.40942','184.0731','385.23','502.29222','503.29564','548.33424','550.32453','551.32481','566.28931','566.79058','568.339'], ['2','1','7','4','1','5','0','18','5','4','1','1','0','0','999'], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), { 'num_res' => 2, 'pcgroup_id' => 1, 'res' => [ { 'id' => 'CA000162', 'exactMass' => '568.42803', 'title' => 'beta,beta-Carotene-2,2\'-diol; FAB-EBEB; MS2; m/z: 568.43; [M]*+', 'formula' => 'C40H56O2', 'score' => '0.904567659364' }, { 'exactMass' => '568.42803', 'id' => 'CA000153', 'score' => '0.620521335460', 'formula' => 'C40H56O2', 'title' => 'Isozeaxanthin; FAB-EBEB; MS2; m/z: 568.43; [M]*+' } ] }, "Method \'searchSpectrum\' works with $server server and return a list of entries from given mzs list /!\\ Bug - Real relative intensity"); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and max = 2 **\n" ; $current_test++; is_deeply( searchSpectrumNBTest( ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['300', '300', '300', '300', '300', '300', '300'], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), 2, 'Method \'searchSpectrum\' works with $server server and return the right number of entries from given mzs list and parameters (max)'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff print "\n** Test $current_test searchSpectrum with a list of mzs, but no intensity (in true very low) and max = 2 **\n" ; $current_test++; is_deeply( searchSpectrumNBTest( ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], [10, 10, 10, 10, 10, 10, 10 ], 'Positive', # mode ['all'], # instrument '2', # max return / only 2 for test 'unit', # unit (unit or ppm) 0.3, # tol with unit = unit / can be also 50 with unit = ppm 50 # cutoff ), 2, 'Method \'searchSpectrum\' works with $server server and return the right number of entries from given mzs list and no intensity'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and no optionnal parameter like instrument, unit, tolerance and cutoff **\n" ; $current_test ++; is_deeply( searchSpectrumNBTest( ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['300', '300', '300', '300', '300', '300', '300'], 'Positive', # mode undef, # instrument '2', # max return / only 2 for test undef, # unit (unit or ppm) undef, # tol with unit = unit / can be also 50 with unit = ppm undef # cutoff ), 2, 'Method \'searchSpectrum\' works with $server server and return the right number of entries from def parameters (instrument, unit, tolerance, cutoff )'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $mzs, $intensities, $ion, $instruments, $max, $unit, $tol, $cutoff, $max print "\n** Test $current_test searchSpectrum with a list of mzs, intensities and no conf parameters for instrument, unit, tolerance and cutoff (value by default) **\n" ; $current_test++; is_deeply( searchSpectrumNBTest( ['273.096', '289.086', '290.118', '291.096', '292.113', '579.169', '580.179'], ['300', '300', '300', '300', '300', '300', '300'], 'Positive', # mode undef, # instrument - ['all'] by default undef, # max return - 0 by default undef, # unit - unit by default undef, # tol - 0.3 (by default) with unit = unit / can be also 50 (by default) with unit = ppm undef # cutoff - 5 by default ), 388, 'Method \'searchSpectrum\' works with $server server and return the right number of entries (363) with undef parameters (instrument, unit, tolerance, cutoff, max )'); ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ARGVTS : $ids print "\n** Test $current_test getPeak with a list ids **\n" ; $current_test++; is_deeply( getPeakTest( ['PR020003', 'FU000001']), [ { 'numPeaks' => '9', 'mzs' => ['207.0897','210.0499','224.5345','225.2768','226.0377','226.9938','227.9228','243.1025','410.0056'], 'intensities' => ['8.488e2','9.442e2','1.093e3','5.294e4','2.896e4','7.015e3','7.870e2','4.024e3','5.620e2'], 'id' => 'PR020003' }, { 'id' => 'FU000001', 'intensities' => ['3.277e5', '3.036e4', '5.812e4', '2.982e5', '5.196e4','4.564e5', '8.939e5','5.537e4'], 'mzs' => ['370.8', '371.4', '532.0', '532.6', '533.3', '694.1', '694.8','695.4'], 'numPeaks' => '8' } ], 'Method \'getPeak\' works with $server server and return the peak lists from given ids list'); print "\n- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n" ; } else { croak "Can\'t launch any test : no sequence clearly defined !!!!\n" ; }