Mercurial > repos > fgiacomoni > hmdb_ms_search
changeset 9:c32280662103 draft
Master branch Updating - - Fxx
| author | fgiacomoni |
|---|---|
| date | Wed, 19 Sep 2018 11:09:30 -0400 |
| parents | 97788e4bf3fc |
| children | 4eb2de7c24d1 |
| files | conf_hmdb.cfg lib/hmdb.pm t/hmdb_managerTest.pl t/lib/hmdbTest.pm wsdl_hmdb.xml |
| diffstat | 5 files changed, 79 insertions(+), 7 deletions(-) [+] |
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--- a/conf_hmdb.cfg Sat Jan 20 17:36:51 2018 -0500 +++ b/conf_hmdb.cfg Wed Sep 19 11:09:30 2018 -0400 @@ -1,11 +1,11 @@ ## Conf file for wsdl_hmdb.pl script # ## Version -- edited by F.Giacomoni -VERSION=2016-11-28 +VERSION=2018-06-13 # ## ARGVT # Hmdb limits per job (max is 700) -HMDB_LIMITS=200 +HMDB_LIMITS=50 ## Maximum query filtered (default is 20 - min : 1 / max 50) HMDB_MAX_QUERY=20 ## Galaxy url for HTML JS and CSS path
--- a/lib/hmdb.pm Sat Jan 20 17:36:51 2018 -0500 +++ b/lib/hmdb.pm Wed Sep 19 11:09:30 2018 -0400 @@ -225,7 +225,7 @@ my $ua = LWP::UserAgent->new( keep_alive => 10 ); $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36"); - $ua->timeout(240); + $ua->timeout(2400) ; my $req = HTTP::Request->new( POST => 'http://specdb.wishartlab.com/ms/search.csv');
--- a/t/hmdb_managerTest.pl Sat Jan 20 17:36:51 2018 -0500 +++ b/t/hmdb_managerTest.pl Wed Sep 19 11:09:30 2018 -0400 @@ -130,6 +130,78 @@ is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ), [], 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ; + + ## Other example... from mz 265.0567515 + print "\n** Test $current_test parse_hmdb_csv_results with mz 265.0567515 and the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; + is_deeply ( parse_hmdb_csv_resultsTest ( + [ + 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', + '265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2', + '265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', + '265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', + '265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', + '265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', + '265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3', + '265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', + '265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', + '265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', + '265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4', + ], + ['265.0567515'], + 5 + ), + [ + [ + { + 'ENTRY_DELTA' => '2', + 'ENTRY_FORMULA' => 'C5H8O2S', + 'ENTRY_ENTRY_ID' => 'HMDB0059667', + 'ENTRY_ADDUCT_MZ' => '265.056276', + 'ENTRY_ADDUCT_TYPE' => '+', + 'ENTRY_CPD_MZ' => '132.02450019', + 'ENTRY_ADDUCT' => '2M+H' + }, + { + 'ENTRY_ADDUCT_MZ' => '265.056128', + 'ENTRY_ENTRY_ID' => 'HMDB0038767', + 'ENTRY_ADDUCT_TYPE' => '+', + 'ENTRY_CPD_MZ' => '726.200729034', + 'ENTRY_ADDUCT' => 'M+3Na', + 'ENTRY_DELTA' => '2', + 'ENTRY_FORMULA' => 'C32H38O19' + }, + { + 'ENTRY_DELTA' => '2', + 'ENTRY_FORMULA' => 'C32H38O19', + 'ENTRY_ENTRY_ID' => 'HMDB0039759', + 'ENTRY_ADDUCT_MZ' => '265.056128', + 'ENTRY_ADDUCT_TYPE' => '+', + 'ENTRY_CPD_MZ' => '726.200729034', + 'ENTRY_ADDUCT' => 'M+3Na' + }, + { + 'ENTRY_FORMULA' => 'C32H38O19', + 'ENTRY_DELTA' => '2', + 'ENTRY_ADDUCT_TYPE' => '+', + 'ENTRY_ADDUCT_MZ' => '265.056128', + 'ENTRY_ENTRY_ID' => 'HMDB0040875', + 'ENTRY_CPD_MZ' => '726.200729034', + 'ENTRY_ADDUCT' => 'M+3Na' + }, + { + 'ENTRY_ADDUCT_TYPE' => '+', + 'ENTRY_ENTRY_ID' => 'HMDB0040878', + 'ENTRY_ADDUCT_MZ' => '265.056128', + 'ENTRY_ADDUCT' => 'M+3Na', + 'ENTRY_CPD_MZ' => '726.200729034', + 'ENTRY_FORMULA' => 'C32H38O19', + 'ENTRY_DELTA' => '2' + } + ] + ], + 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; + + }
--- a/t/lib/hmdbTest.pm Sat Jan 20 17:36:51 2018 -0500 +++ b/t/lib/hmdbTest.pm Wed Sep 19 11:09:30 2018 -0400 @@ -75,7 +75,7 @@ my $oHmdb = lib::hmdb->new() ; my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max) ; ## hash format result - + print Dumper $result ; return($result) ; }
--- a/wsdl_hmdb.xml Sat Jan 20 17:36:51 2018 -0500 +++ b/wsdl_hmdb.xml Wed Sep 19 11:09:30 2018 -0400 @@ -8,9 +8,9 @@ <requirement type="package" version="6.15">perl-lwp-simple</requirement> <requirement type="package" version="6.15">perl-libwww-perl</requirement> <requirement type="package" version="2.95">perl-html-template</requirement> - <requirement type="package" version="1.71">perl-uri</requirement> - <requirement type="package" version="1.33">perl-text-csv</requirement> - <requirement type="package" version="3.49">perl-xml-twig</requirement> + <requirement type="package" version="1.74">perl-uri</requirement> + <requirement type="package" version="1.97">perl-text-csv</requirement> + <requirement type="package" version="3.52">perl-xml-twig</requirement> </requirements> <stdio>