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Changeset 10:4eb2de7c24d1 (2018-10-01)

Previous changeset 9:c32280662103 (2018-09-19) Next changeset 11:ecb6a28552d6 (2018-10-01)

Commit message:
Master branch Updating - - Fxx

modified:
t/hmdb_managerTest.pl
t/lib/hmdbTest.pm
test-data/out_test03.html
test-data/out_test03.tabular
test-data/out_test03.txt
wsdl_hmdb.pl
wsdl_hmdb.xml

diff -r c32280662103 -r 4eb2de7c24d1 t/hmdb_managerTest.pl
--- a/t/hmdb_managerTest.pl Wed Sep 19 11:09:30 2018 -0400
+++ b/t/hmdb_managerTest.pl Mon Oct 01 10:36:30 2018 -0400

[

@@ -57,13 +57,49 @@
#          '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
#          '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
## Update format - 2018-01-19... HMDB V04
- '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
- '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
- '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
- '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
- '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
- '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
- '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
+# '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
+# '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
+# '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
+# '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
+# '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
+# '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
+# '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
+ ## Update results - 2018-09-20... HMDBv4
+ #'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
+          '175.01,HMDB0149376,"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
+          '175.01,HMDB0149375,"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
+          '175.01,HMDB0149419,"2-{[5,8-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
+          '175.01,HMDB0149418,"2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
+          '175.01,HMDB0149392,"2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
+          '175.01,HMDB0149391,"2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
+          '175.01,HMDB0000257,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
+          '175.01,HMDB0060293,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
+          '175.01,HMDB0141391,{4-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
+          '175.01,HMDB0141389,{3-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
+          '175.01,HMDB0135622,{4-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
+          '175.01,HMDB0135448,{3-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
+          '175.01,HMDB0240280,Methanesulfonic acid,C11145,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4',
+          '175.01,HMDB0003745,Coenzyme m,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
+          '175.01,HMDB0142159,[2-hydroxy-2-(2-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142160,[2-hydroxy-1-(2-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142162,"[3-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142166,"[4-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142164,[2-hydroxy-1-(3-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142163,[2-hydroxy-2-(3-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142167,[2-hydroxy-2-(4-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0142168,[2-hydroxy-1-(4-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0129951,"{3-[2-(3,5-dihydroxyphenyl)ethyl]phenyl}oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
+          '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
+          '175.01,HMDB0033657,"11,15-Dihydroxy-6,8,20-trioxapentacyclo[10.8.0.0²,⁹.0³,⁷.0¹⁴,¹⁹]icosa-1(12),2(9),4,10,14,16,18-heptaen-13-one",C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
+          '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)-2H-furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
+          '175.01,HMDB0155176,5-Hydroxy-6-hydrouracil,n/a,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6',
+          '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
+          '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
+          '420.16,HMDB0160148,"6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
+          '420.16,HMDB0160149,"6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
+          '420.16,HMDB0165020,"6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
+          '420.16,HMDB0175397,"6-{[3-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
+          '420.16,HMDB0184353,"6-[(4-carboxy-3,3-dimethylbutanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2'
         ],
'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb');

diff -r c32280662103 -r 4eb2de7c24d1 t/lib/hmdbTest.pm
--- a/t/lib/hmdbTest.pm Wed Sep 19 11:09:30 2018 -0400
+++ b/t/lib/hmdbTest.pm Mon Oct 01 10:36:30 2018 -0400

@@ -45,6 +45,7 @@

my $oHmdb = lib::hmdb->new() ;
my $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
+ print Dumper $hmdb_pages ;
return ($hmdb_pages) ;
}

diff -r c32280662103 -r 4eb2de7c24d1 test-data/out_test03.html
--- a/test-data/out_test03.html Wed Sep 19 11:09:30 2018 -0400
+++ b/test-data/out_test03.html Mon Oct 01 10:36:30 2018 -0400

b'@@ -1,1 +1,1 @@\n-<?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style type="text/css">body {padding-top: 70px}div.lm-table-warning { font-size: 1.4em; font-weight: bold; padding-right: 25px; color: #21536a; margin-left: 3px;}tr.green td {background-color: #eaf2d3; color: black;}tr.blank td {background-color: #9999CC; color: black;}table {font-family:\'Trebuchet MS\',Arial,Helvetica,sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size: 1.2em;text-align: center;padding-top: 5px;padding-bottom: 10px;background-color: #a7c942;color: #ffffff;}td.ca {text-align:center;}footer { margin: 50px 0;}</style><script>function test(pageNumber){ var page="#page-id-"+pageNumber; $(\'.select\').hide() ; $(page).show()}</script></head><body><div class="container"><div class="lm-table-warning">Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><table id="detail_table" class="detail"><col style="width:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >175.01</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Hydroxidodioxidosulfidosulfate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060293" target="_blank" class="btn">HMDB0060293</a></td><td class="ca">H2O3S2</td><td class="ca">113.94453531</td><td class="ca">M+IsoProp+H</td><td class="ca">+</td><td class="ca">175.009875</td><td class="ca">1</td><td class="ca">InChI=1S/H2O3S2/c1-5(2,3)4/h(H2,1,2,3,4)</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Mesna</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0003745" target="_blank" class="btn">HMDB0003745</a></td><td class="ca">C2H6O3S2</td><td class="ca">141.975835438</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">175.009324</td><td class="ca">4</td><td class="ca">InChI=1S/C2H6O3S2/c3-7(4,5)2-1-6/h6H,1-2H2,(H,3,4,5)</td><td class="ca">-1.53</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Silicic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031436" target="_blank" class="btn">HMDB0031436</a></td><td class="ca">H4O4Si</td><td c'..b'td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0168231" target="_blank" class="btn">HMDB0168231</a></td><td class="ca">C25H20O9</td><td class="ca">464.110732224</td><td class="ca">2M+2H+3H2O</td><td class="ca">+</td><td class="ca">956.244584</td><td class="ca">6</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0138858" target="_blank" class="btn">HMDB0138858</a></td><td class="ca">C25H20O9</td><td class="ca">464.110732224</td><td class="ca">2M+2H+3H2O</td><td class="ca">+</td><td class="ca">956.244584</td><td class="ca">6</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0168237" target="_blank" class="btn">HMDB0168237</a></td><td class="ca">C25H20O9</td><td class="ca">464.110732224</td><td class="ca">2M+2H+3H2O</td><td class="ca">+</td><td class="ca">956.244584</td><td class="ca">6</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >1100.45</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">NPC</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060499" target="_blank" class="btn">HMDB0060499</a></td><td class="ca">C28H30N4O6</td><td class="ca">518.216534712</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.448834</td><td class="ca">1</td><td class="ca">InChI=1S/C28H30N4O6/c1-3-17-18-11-16(38-27(35)31-9-7-15(29)8-10-31)5-6-22(18)30-24-19(17)13-32-23(24)12-21-20(25(32)33)14-37-26(34)28(21,36)4-2/h5-6,11-12,15,36H,3-4,7-10,13-14,29H2,1-2H3/t28-/m0/s1</td><td class="ca">2.40</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0158990" target="_blank" class="btn">HMDB0158990</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0158993" target="_blank" class="btn">HMDB0158993</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0157972" target="_blank" class="btn">HMDB0157972</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0158992" target="_blank" class="btn">HMDB0158992</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NA</td><td class="ca">NA</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r c32280662103 -r 4eb2de7c24d1 test-data/out_test03.tabular
--- a/test-data/out_test03.tabular Wed Sep 19 11:09:30 2018 -0400
+++ b/test-data/out_test03.tabular Mon Oct 01 10:36:30 2018 -0400

[

@@ -1,31 +1,31 @@
ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 1 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB0060293
-mz_00001 175.01 4 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB0003745
-mz_00001 175.01 5 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB0031436
-mz_00001 175.01 5 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0033657
-mz_00001 175.01 5 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0035230
+mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376
+mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375
+mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391
+mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392
+mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418
+mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116
+mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564
mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043
mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086
mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472
-mz_00002 238.19 4 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0005812
-mz_00002 238.19 4 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0035861
mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836
mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838
-mz_00003 420.16 3 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB0033374
-mz_00003 420.16 3 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0000590
-mz_00003 420.16 3 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0001138
+mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148
+mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149
+mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020
+mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081
mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
-mz_00004 780.32 7 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB0035940
-mz_00004 780.32 10 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0033906
-mz_00004 780.32 10 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0039032
-mz_00004 780.32 10 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0032731
-mz_00005 956.25 6 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0035451
-mz_00005 956.25 6 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0038095
-mz_00005 956.25 9 [UNKNOWN] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0153300
-mz_00005 956.25 9 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0040803
-mz_00005 956.25 9 [2-(4-hydroxy-3-methoxyphenyl)-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0141944
+mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078
+mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083
+mz_00004 780.32 3 [UNKNOWN] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342
+mz_00005 956.25 5 [PRE] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300
+mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193
+mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231
+mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858
+mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237
mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499
-mz_00006 1100.45 4 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB0032198
-mz_00006 1100.45 13 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006568
-mz_00006 1100.45 13 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0002060
-mz_00006 1100.45 13 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006582
+mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990
+mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993
+mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972
+mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992

diff -r c32280662103 -r 4eb2de7c24d1 test-data/out_test03.txt
--- a/test-data/out_test03.txt Wed Sep 19 11:09:30 2018 -0400
+++ b/test-data/out_test03.txt Mon Oct 01 10:36:30 2018 -0400

[

diff -r c32280662103 -r 4eb2de7c24d1 wsdl_hmdb.pl
--- a/wsdl_hmdb.pl Wed Sep 19 11:09:30 2018 -0400
+++ b/wsdl_hmdb.pl Mon Oct 01 10:36:30 2018 -0400

@@ -123,7 +123,7 @@
$oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution

foreach my $mzs ( @{$submasses} ) {
- print Dumper $mzs ;
+# print Dumper $mzs ;
my $result = undef ;
my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
$hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
@@ -139,9 +139,9 @@

## Map metabocards with results (add supplementary data)

- print Dumper $results ;
- print Dumper $hmdb_ids ;
- print Dumper $metabocard_features ;
+# print Dumper $results ;
+# print Dumper $hmdb_ids ;
+# print Dumper $metabocard_features ;

if ( ( defined $results ) and ( defined $metabocard_features ) ) {
$results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;

diff -r c32280662103 -r 4eb2de7c24d1 wsdl_hmdb.xml
--- a/wsdl_hmdb.xml Wed Sep 19 11:09:30 2018 -0400
+++ b/wsdl_hmdb.xml Mon Oct 01 10:36:30 2018 -0400

@@ -4,10 +4,10 @@
   </description>

   <requirements>
+      <requirement type="package" version="2.97">perl-html-template</requirement>
       <requirement type="package" version="1.19">perl-soap-lite</requirement>
       <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="1.74">perl-uri</requirement>
       <requirement type="package" version="1.97">perl-text-csv</requirement>
       <requirement type="package" version="3.52">perl-xml-twig</requirement>
@@ -91,8 +91,9 @@
   </outputs>

   <tests>
+
+   <!~~test 01 no result - fake-mzrt-input-with-id ~~>
    <param name="choice" value="YES"/>
    <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
    <param name="header_choice" value="yes"/>
@@ -106,7 +107,7 @@
    <output name="HmdbOutXlsx" file="out_test01.txt"/>
    </test>
    <test>
-   
+   <!~~test 02 : some results - with-mzrt-input-with-id file~~>
    <param name="choice" value="YES"/>
    <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
    <param name="header_choice" value="yes"/>
@@ -119,6 +120,7 @@
    <output name="HmdbOutWeb" file="out_test02.html"/>
    <output name="HmdbOutXlsx" file="out_test02.txt"/>
    </test>
+ -->
    <test>
    
    <param name="choice" value="NO"/>