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Changeset 24:d8e2ede293a6 (2022-05-19)

Previous changeset 23:2d8a310e86ce (2022-05-19) Next changeset 25:8f7546d0b925 (2022-07-05)

Commit message:
Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx

modified:
conf_hmdb.cfg
lib/hmdb.pm
test-data/out_test02.html
test-data/out_test02.tabular
test-data/out_test02.txt
test-data/out_test03.html
test-data/out_test03.tabular
test-data/out_test03.txt
test-data/out_test04.html
test-data/out_test04.tabular
test-data/out_test04.txt
wsdl_hmdb.pl
wsdl_hmdb.xml

diff -r 2d8a310e86ce -r d8e2ede293a6 conf_hmdb.cfg
--- a/conf_hmdb.cfg Thu May 19 13:43:09 2022 +0000
+++ b/conf_hmdb.cfg Thu May 19 14:41:34 2022 +0000

@@ -1,7 +1,7 @@
## Conf file for wsdl_hmdb.pl script
#
## Version -- edited by F.Giacomoni
-VERSION=1.6.0
+VERSION=1.7.1
#
## ARGVT
# Hmdb limits per job (max is 700)
@@ -14,4 +14,4 @@
#
## HTML OUTPUT :
HTML_ENTRIES_PER_PAGE=4
-HMDB_METABOCARD_URL=http://www.hmdb.ca/metabolites/
+HMDB_METABOCARD_URL=https://hmdb.ca/metabolites/

diff -r 2d8a310e86ce -r d8e2ede293a6 lib/hmdb.pm
--- a/lib/hmdb.pm Thu May 19 13:43:09 2022 +0000
+++ b/lib/hmdb.pm Thu May 19 14:41:34 2022 +0000

[

@@ -710,7 +710,7 @@
#query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value',

      if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),(\d*)/   ) {
-     print "$line\n" ;
+     #print "$line\n" ;
      #if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a|\s+]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/  ) {
      my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;

diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test02.html
--- a/test-data/out_test02.html Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test02.html Thu May 19 14:41:34 2022 +0000

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) = 0.001</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 (ppm)</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" >7.02080998</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Beryllium</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0002387" target="_blank" class="btn">HMDB0002387</a></td><td class="ca">Be</td><td class="ca">9.012182135</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">7.02033</td><td class="ca">68</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00002</td><td id="2" class="ca" >75.05547146</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">glycinamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062472" target="_blank" class="btn">HMDB0062472</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012824</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-Nitrosodimethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031419" target="_blank" class="btn">HMDB00'..b'</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-Methoxyethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245205" target="_blank" class="btn">HMDB0245205</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413914</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(E)-1-Propenol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243637" target="_blank" class="btn">HMDB0243637</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.075688</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Methyl vinyl ether</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0254619" target="_blank" class="btn">HMDB0254619</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.075688</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >76.07593168</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-(2-Hydroxypropan-2-ylamino)propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257796" target="_blank" class="btn">HMDB0257796</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Aminopropanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248330" target="_blank" class="btn">HMDB0248330</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413914</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-Methoxyethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245205" target="_blank" class="btn">HMDB0245205</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413914</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">(E)-1-Propenol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243637" target="_blank" class="btn">HMDB0243637</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.075688</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Methyl vinyl ether</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0254619" target="_blank" class="btn">HMDB0254619</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.075688</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</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 2d8a310e86ce -r d8e2ede293a6 test-data/out_test02.tabular
--- a/test-data/out_test02.tabular Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test02.tabular Thu May 19 14:41:34 2022 +0000

[

@@ -1,7 +1,7 @@
id mz rt hmdb(delta::name::mz::formula::adduct::id)
-1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387
-2 75.05547146 0.658528069 "2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222"
-3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 1::[Ethanol]::46.041864814::C2H6O::[2M+H-H2O]::HMDB0000108 | 2::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[""1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether""]::74.073164942::C4H10O::[M+H]::HMDB0062326"
-4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Iminodiacetic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0011753 | 2::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB0000123 | 2::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB0014691"
-5 76.07584477 50.51249853 "2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-monomethylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB0031558"
-6 76.07593168 0.149308136 "3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-monomethylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB0031558"
+1 7.02080998 49.38210915 NONE
+2 75.05547146 0.658528069 "2::[O-Methylisourea]::74.048012821::C2H6N2O::[M+H]::HMDB0255861 | 2::[N-Propyl-N-nitrosourea]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0255236 | 2::[N-METHYL-N-FORMYLHYDRAZINE]::74.048012821::C2H6N2O::[M+H]::HMDB0255179 | 2::[Asparaginamide]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0248665 | 2::[N'-Hydroxyethanimidamide]::74.048012821::C2H6N2O::[M+H]::HMDB0243752"
+3 75.08059797 1743.94267 "2::[""Propan-2,2-diyl""]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0251402 | 5::[Methylene]::14.015650064::CH2::[M+IsoProp+H]::HMDB0249629 | 2::[Cyclopropane]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0250673 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 2::[Propylene]::42.046950192::C3H6::[M+CH3OH+H]::HMDB0256839"
+4 76.03942694 51.23158899 "5::[Glutamic acid diethyl ester]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0252807 | 2::[Methylcarbonyloxy]::58.005479304::C2H2O2::[M+NH4]::HMDB0249651 | 2::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+H]::HMDB0248304 | 2::[2-Hydroxyacetamide]::75.032028405::C2H5NO2::[M+H]::HMDB0245149 | 5::[1-Carboxyethylisoleucine]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0242158"
+5 76.07584477 50.51249853 "2::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 2::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 2::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 2::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637 | 2::[Methyl vinyl ether]::58.041864813::C3H6O::[M+NH4]::HMDB0254619"
+6 76.07593168 0.149308136 "3::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 3::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 3::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 3::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637 | 3::[Methyl vinyl ether]::58.041864813::C3H6O::[M+NH4]::HMDB0254619"

diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test02.txt
--- a/test-data/out_test02.txt Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test02.txt Thu May 19 14:41:34 2022 +0000

[

@@ -1,27 +1,27 @@
ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387
-mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472
-mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419
-mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428
-mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064
-mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222
+mz_00001 7.02080998 0 UNKNOWN N/A N/A N/A N/A N/A
+mz_00002 75.05547146 2 [O-Methylisourea] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0255861
+mz_00002 75.05547146 2 [N-Propyl-N-nitrosourea] 131.069476542 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0255236
+mz_00002 75.05547146 2 [N-METHYL-N-FORMYLHYDRAZINE] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0255179
+mz_00002 75.05547146 2 [Asparaginamide] 131.069476542 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0248665
+mz_00002 75.05547146 2 [N'-Hydroxyethanimidamide] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0243752
+mz_00003 75.08059797 2 ["Propan-2,2-diyl"] 42.046950193 C3H6 [M+CH3OH+H] 75.080439 HMDB0251402
+mz_00003 75.08059797 5 [Methylene] 14.015650064 CH2 [M+IsoProp+H] 75.08099 HMDB0249629
+mz_00003 75.08059797 2 [Cyclopropane] 42.046950193 C3H6 [M+CH3OH+H] 75.080439 HMDB0250673
mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250
-mz_00003 75.08059797 1 [Ethanol] 46.041864814 C2H6O [2M+H-H2O] 75.08053 HMDB0000108
-mz_00003 75.08059797 2 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456
-mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327
-mz_00003 75.08059797 2 ["1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether"] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062326
-mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191
-mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239
-mz_00004 76.03942694 2 [Iminodiacetic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0011753
-mz_00004 76.03942694 2 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0000123
-mz_00004 76.03942694 2 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0014691
-mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
-mz_00005 76.07584477 2 [N-monomethylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
-mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925
-mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
-mz_00005 76.07584477 2 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031558
-mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
-mz_00006 76.07593168 3 [N-monomethylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
-mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925
-mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
-mz_00006 76.07593168 3 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031558
+mz_00003 75.08059797 2 [Propylene] 42.046950192 C3H6 [M+CH3OH+H] 75.080439 HMDB0256839
+mz_00004 76.03942694 5 [Glutamic acid diethyl ester] 203.115758031 C9H17NO4 [M+2H+Na] 76.039843 HMDB0252807
+mz_00004 76.03942694 2 [Methylcarbonyloxy] 58.005479304 C2H2O2 [M+NH4] 76.039302 HMDB0249651
+mz_00004 76.03942694 2 [o-Acetylhydroxylamine] 75.032028405 C2H5NO2 [M+H] 76.039304 HMDB0248304
+mz_00004 76.03942694 2 [2-Hydroxyacetamide] 75.032028405 C2H5NO2 [M+H] 76.039304 HMDB0245149
+mz_00004 76.03942694 5 [1-Carboxyethylisoleucine] 203.115758031 C9H17NO4 [M+2H+Na] 76.039843 HMDB0242158
+mz_00005 76.07584477 2 [2-(2-Hydroxypropan-2-ylamino)propan-2-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0257796
+mz_00005 76.07584477 2 [Aminopropanol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0248330
+mz_00005 76.07584477 2 [2-Methoxyethylamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0245205
+mz_00005 76.07584477 2 [(E)-1-Propenol] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0243637
+mz_00005 76.07584477 2 [Methyl vinyl ether] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0254619
+mz_00006 76.07593168 3 [2-(2-Hydroxypropan-2-ylamino)propan-2-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0257796
+mz_00006 76.07593168 3 [Aminopropanol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0248330
+mz_00006 76.07593168 3 [2-Methoxyethylamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0245205
+mz_00006 76.07593168 3 [(E)-1-Propenol] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0243637
+mz_00006 76.07593168 3 [Methyl vinyl ether] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0254619

diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test03.html
--- a/test-data/out_test03.html Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test03.html Thu May 19 14:41:34 2022 +0000

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 (ppm)</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">Phenol sulphate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060015" target="_blank" class="btn">HMDB0060015</a></td><td class="ca">C6H6O4S</td><td class="ca">173.99867937</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">175.005955</td><td class="ca">23</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">trans-Aconitic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000958" target="_blank" class="btn">HMDB0000958</a></td><td class="ca">C6H6O6</td><td class="ca">174.016437924</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">175.023714</td><td class="ca">78</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">cis-Aconitic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000072" target="_blank" class="btn">HMDB0000072</a></td><td class="ca">C6H6O6</td><td class="ca">174.016437924</td><td class="ca">M+H</td><td class="ca">+</t'..b'<td class="ca">M+H</td><td class="ca">+</td><td class="ca">420.150702</td><td class="ca">22</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"Glycine, L-gamma-glutamyl-2-(1-methyl-4-(nitrosothio)-4-piperidinyl)glycyl-"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0253933" target="_blank" class="btn">HMDB0253933</a></td><td class="ca">C15H25N5O7S</td><td class="ca">419.147469339</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">420.154745</td><td class="ca">13</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Dolutegravir</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0251580" target="_blank" class="btn">HMDB0251580</a></td><td class="ca">C20H19F2N3O5</td><td class="ca">419.12927705</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">420.136553</td><td class="ca">56</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Acorafloxacin</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0247964" target="_blank" class="btn">HMDB0247964</a></td><td class="ca">C21H23F2N3O4</td><td class="ca">419.165662559</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">420.172939</td><td class="ca">31</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >780.32</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Ravtansine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0247402" target="_blank" class="btn">HMDB0247402</a></td><td class="ca">C38H54ClN3O10S</td><td class="ca">779.3218438</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">780.32912</td><td class="ca">12</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">3\'-Sialyl-3-fucosyllactose</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0006606" target="_blank" class="btn">HMDB0006606</a></td><td class="ca">C29H49NO23</td><td class="ca">779.269536879</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">780.276813</td><td class="ca">55</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >956.25</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">jasmonoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0304397" target="_blank" class="btn">HMDB0304397</a></td><td class="ca">C33H48N7O18P3S</td><td class="ca">955.201134221</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">956.20841</td><td class="ca">43</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</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">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</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 2d8a310e86ce -r d8e2ede293a6 test-data/out_test03.tabular
--- a/test-data/out_test03.tabular Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test03.tabular Thu May 19 14:41:34 2022 +0000

[

@@ -1,11 +1,19 @@
ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 23 [Phenol sulphate] 173.99867937 C6H6O4S [M+H] 175.005955 HMDB0060015
-mz_00001 175.01 78 [trans-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000958
-mz_00001 175.01 78 [cis-Aconitic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0000072
-mz_00001 175.01 78 [Dehydroascorbic acid] 174.016437924 C6H6O6 [M+H] 175.023714 HMDB0001264
-mz_00001 175.01 78 [dehydroascorbide(1-)] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0062706
-mz_00002 238.19 0 UNKNOWN N/A N/A N/A N/A N/A
-mz_00003 420.16 57 [Fenvalerate] 419.128821282 C25H22ClNO3 [M+H] 420.136097 HMDB0031791
+mz_00001 175.01 271 [Trinitrosotrimethylenetriamine] 174.050138077 C3H6N6O3 [M+H] 175.057414 HMDB0259249
+mz_00001 175.01 166 ["Naphthalene-1,2,4-trione"] 174.031694053 C10H6O3 [M+H] 175.03897 HMDB0257698
+mz_00001 175.01 70 [Phenyl phosphonothioate] 173.990437637 C6H7O2PS [M+H] 174.997714 HMDB0256424
+mz_00001 175.01 71 [p-TOLUENESULFONYL FLUORIDE] 174.015078802 C7H7FO2S [M+H] 175.022355 HMDB0256057
+mz_00001 175.01 78 [Aconitic acid] 174.016437913 C6H6O6 [M+H] 175.023714 HMDB0247961
+mz_00002 238.19 41 ["N,N-di-n-propyldopamine"] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0255249
+mz_00002 238.19 6 [Ethoxybenzyl diethylenetriamine] 237.184112373 C13H23N3O [M+H] 238.191388 HMDB0252022
+mz_00002 238.19 41 [Deacetylmoxisylyte] 237.172878985 C14H23NO2 [M+H] 238.180155 HMDB0250903
+mz_00002 238.19 194 [viloxazine] 237.136493476 C13H19NO3 [M+H] 238.143769 HMDB0259807
+mz_00003 420.16 87 [Cligosiban] 419.1160454 C19H19ClFN5O3 [M+H] 420.123321 HMDB0256366
+mz_00003 420.16 22 [Perphenazine sulfoxide] 419.143426 C21H26ClN3O2S [M+H] 420.150702 HMDB0256352
+mz_00003 420.16 13 ["Glycine, L-gamma-glutamyl-2-(1-methyl-4-(nitrosothio)-4-piperidinyl)glycyl-"] 419.147469339 C15H25N5O7S [M+H] 420.154745 HMDB0253933
+mz_00003 420.16 56 [Dolutegravir] 419.12927705 C20H19F2N3O5 [M+H] 420.136553 HMDB0251580
+mz_00003 420.16 31 [Acorafloxacin] 419.165662559 C21H23F2N3O4 [M+H] 420.172939 HMDB0247964
+mz_00004 780.32 12 [Ravtansine] 779.3218438 C38H54ClN3O10S [M+H] 780.32912 HMDB0247402
mz_00004 780.32 55 [3'-Sialyl-3-fucosyllactose] 779.269536879 C29H49NO23 [M+H] 780.276813 HMDB0006606
-mz_00005 956.25 0 UNKNOWN N/A N/A N/A N/A N/A
+mz_00005 956.25 43 [jasmonoyl-CoA] 955.201134221 C33H48N7O18P3S [M+H] 956.20841 HMDB0304397
mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A

diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test03.txt
--- a/test-data/out_test03.txt Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test03.txt Thu May 19 14:41:34 2022 +0000

[

diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test04.html
--- a/test-data/out_test04.html Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test04.html Thu May 19 14:41:34 2022 +0000

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 (ppm)</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">Mercaptopurine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0015167" target="_blank" class="btn">HMDB0015167</a></td><td class="ca">C5H4N4S</td><td class="ca">152.015666838</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.004885</td><td class="ca">29</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">S-Methyl benzenecarbothioate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0029694" target="_blank" class="btn">HMDB0029694</a></td><td class="ca">C8H8OS</td><td class="ca">152.029585568</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.018804</td><td class="ca">50</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"6,8-Dihydroxypurine"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0001182" target="_blank" class="btn">HMDB0001182</a></td><td class="ca">C5H4N4O2</td><td class="ca">152.033425392</td><td class="ca">M+Na</td><'..b' class="ca">397.153874872</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">420.143093</td><td class="ca">40</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >780.32</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Vaniprevir</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0259762" target="_blank" class="btn">HMDB0259762</a></td><td class="ca">C38H55N5O9S</td><td class="ca">757.372049545</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">780.361268</td><td class="ca">53</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >956.25</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">undec-10-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300959" target="_blank" class="btn">HMDB0300959</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Undec-8-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300958" target="_blank" class="btn">HMDB0300958</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Undec-9-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300957" target="_blank" class="btn">HMDB0300957</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Undec-3-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300956" target="_blank" class="btn">HMDB0300956</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(7E)-Undec-7-enoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0300955" target="_blank" class="btn">HMDB0300955</a></td><td class="ca">C32H54N7O17P3S</td><td class="ca">933.250975475</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.240193</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</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">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</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 2d8a310e86ce -r d8e2ede293a6 test-data/out_test04.tabular
--- a/test-data/out_test04.tabular Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test04.tabular Thu May 19 14:41:34 2022 +0000

[

@@ -1,16 +1,23 @@
ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167
-mz_00001 175.01 50 [S-Methyl benzenecarbothioate] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694
-mz_00001 175.01 72 ["6,8-Dihydroxypurine"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182
-mz_00001 175.01 72 [Oxypurinol] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000786
-mz_00001 175.01 72 [Xanthine] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0000292
-mz_00002 238.19 49 [Heptanoylcholine] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239
-mz_00002 238.19 140 [Fencamfamine] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508
-mz_00002 238.19 148 [Solamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202
+mz_00001 175.01 280 [4-Hydrazinylpyridine-3-carboxamide] 152.069810894 C6H8N4O [M+Na] 175.059029 HMDB0258083
+mz_00001 175.01 29 [9-Sulfanylpurine] 152.015667319 C5H4N4S [M+Na] 175.004885 HMDB0257842
+mz_00001 175.01 50 [S-Phenyl thioacetate] 152.029586052 C8H8OS [M+Na] 175.018804 HMDB0257424
+mz_00001 175.01 216 ["n-methyl-6-oxo-1,6-dihydropyridine-3-carboxamide"] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0255171
+mz_00001 175.01 216 [Methyl pyridone carboxamide] 152.058577506 C7H8N2O2 [M+Na] 175.047796 HMDB0254609
+mz_00002 238.19 204 [Ethyl butylacetylaminopropionate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0246904
+mz_00002 238.19 204 [Hexaminolevulinate] 215.15214354 C11H21NO3 [M+Na] 238.141362 HMDB0253144
+mz_00002 238.19 149 [œâ-hydroxylaurate] 215.165268181 C12H23O3 [M+Na] 238.154486 HMDB0304547
mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817
mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279
-mz_00003 420.16 43 [Simulansamide] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435
-mz_00004 780.32 0 UNKNOWN N/A N/A N/A N/A N/A
-mz_00005 956.25 36 ["(2S,3S,4R,5R,6R)-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-4-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4,5-dihydroxy-3-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-(sulfooxy)oxan-2-yl]oxy}oxane-2-carboxylic acid"] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476
-mz_00005 956.25 48 [(3S)-3-isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370
+mz_00003 420.16 93 ["N-Acetyl-9-aminominocycline, (4R)-"] 397.210052342 C20H31NO7 [M+Na] 420.19927 HMDB0259457
+mz_00003 420.16 22 [Reduced ketanserin] 397.180169808 C22H24FN3O3 [M+Na] 420.169388 HMDB0257133
+mz_00003 420.16 58 ["1,2,4-Triazolo(4,3-b)pyridazine, 7-cyclobutyl-3-(2,6-difluorophenyl)-6-((1-methyl-1H-1,2,4-triazol-5-yl)methoxy)-"] 397.146264521 C19H17F2N7O [M+Na] 420.135483 HMDB0254773
+mz_00003 420.16 4 [6-[[3-Fluoro-5-(4-methoxyoxan-4-yl)phenoxy]methyl]-1-methylquinolin-2-one] 397.16893642 C23H24FNO4 [M+Na] 420.158154 HMDB0253359
+mz_00003 420.16 40 [CI-1044] 397.153874872 C23H19N5O2 [M+Na] 420.143093 HMDB0250223
+mz_00004 780.32 53 [Vaniprevir] 757.372049545 C38H55N5O9S [M+Na] 780.361268 HMDB0259762
+mz_00005 956.25 10 [undec-10-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300959
+mz_00005 956.25 10 [Undec-8-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300958
+mz_00005 956.25 10 [Undec-9-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300957
+mz_00005 956.25 10 [Undec-3-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300956
+mz_00005 956.25 10 [(7E)-Undec-7-enoyl-CoA] 933.250975475 C32H54N7O17P3S [M+Na] 956.240193 HMDB0300955
mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A

diff -r 2d8a310e86ce -r d8e2ede293a6 test-data/out_test04.txt
--- a/test-data/out_test04.txt Thu May 19 13:43:09 2022 +0000
+++ b/test-data/out_test04.txt Thu May 19 14:41:34 2022 +0000

[

diff -r 2d8a310e86ce -r d8e2ede293a6 wsdl_hmdb.pl
--- a/wsdl_hmdb.pl Thu May 19 13:43:09 2022 +0000
+++ b/wsdl_hmdb.pl Thu May 19 14:41:34 2022 +0000

@@ -49,7 +49,7 @@
"output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results )
"output_html|v:s" => \$out_html, ## option : path to the results view (output2)
"output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output
- #"advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
+ "advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
"verbose:i" => \$VERBOSE, ## VERBOSE Of the tool
) ;

@@ -160,7 +160,7 @@

## hard modification with $max_query fixed at 1000 !!! Need to be refactoring
## Cutof will be done in next method after URI check
- ($result) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result
+ ($result) = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, 1000) ; ## hash format result

## This previous step return results with cutoff on the number of entries returned !

@@ -216,7 +216,7 @@
($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;

- print Dumper $tbody_object ;
+ # print Dumper $tbody_object ;

my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ;

diff -r 2d8a310e86ce -r d8e2ede293a6 wsdl_hmdb.xml
--- a/wsdl_hmdb.xml Thu May 19 13:43:09 2022 +0000
+++ b/wsdl_hmdb.xml Thu May 19 14:41:34 2022 +0000

@@ -1,6 +1,6 @@
-<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.0">
+<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.1">
   <description>
-        search by masses on HMDB online LCMS bank
+        search by masses on HMDB v5 online LCMS bank
   </description>

   <requirements>
@@ -29,10 +29,10 @@
                 -nblineheader "${$input_type.header.nbHeader}"
             #end if
             -colfactor "${input_type.colfactor}"
-            -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx"
+            -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xlsx "$HmdbOutXlsx"
         #else:
             -mass "${input_type.mass}"
-            -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
+            -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xlsx "$HmdbOutXlsx2"
         #end if

         -mode "${mode_type.mode}"
@@ -377,7 +377,7 @@

.. class:: warningmark

-And their "W4M courses 2021":
+And their "W4M courses 2022":
  | Using Galaxy4Metabolomics - W4M table format for Galaxy
  | Annotation Banks - Annotation