Repository 'hmdb_ms_search'
hg clone https://toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search

Changeset 22:453fbe98925a (2020-11-20)
Previous changeset 21:63ba1cb240b7 (2019-02-14) Next changeset 23:2d8a310e86ce (2022-05-19)
Commit message:
" master branch Updating with tag :CI_COMMIT_TAG - - Fxx"
modified:
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
added:
Dockerfile
b
diff -r 63ba1cb240b7 -r 453fbe98925a Dockerfile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile Fri Nov 20 17:29:18 2020 +0000
[
@@ -0,0 +1,53 @@
+# ref install: ubuntu 20.04
+FROM ubuntu:20.04
+
+# init var
+ARG DEBIAN_FRONTEND=noninteractive
+
+# set author
+MAINTAINER Franck Giacomoni <franck.giacomoni.fr>
+
+### 
+### [CONTAINER CORE FUNCTIONS]: 
+###   xxxx
+###   xxxx
+### [NOTES] 
+###   xxxx
+
+ENV PATH /opt/conda/bin:$PATH
+
+RUN apt-get -y update &&\
+    apt-get -y install build-essential \
+        cpanminus \
+        gzip \
+        wget \
+        bzip2 \
+        ca-certificates \
+        libglib2.0-0  \
+        libxext6  \
+        libsm6  \
+        libxrender1 \
+        libtext-csv-perl \
+        libxml-twig-perl \
+        libfile-share-perl
+
+RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \
+    /bin/bash ~/anaconda.sh -b -p /opt/conda && \
+    rm ~/anaconda.sh && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+RUN cpan install ExtUtils::MakeMaker && \
+    cpan install File::ShareDir::Install && \
+    cpan install Module::Release && \
+    cpan install Archive::Zip && \
+    apt -y install git &&\
+    apt -y install python3 python3-pip && \
+    apt -y install virtualenv && \
+    pip install "pip>=7" && \
+    pip install -U git+git://github.com/galaxyproject/planemo.git && \
+    apt-get autoremove -y && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
b
diff -r 63ba1cb240b7 -r 453fbe98925a lib/hmdb.pm
--- a/lib/hmdb.pm Thu Feb 14 08:36:52 2019 -0500
+++ b/lib/hmdb.pm Fri Nov 20 17:29:18 2020 +0000
b
@@ -222,6 +222,55 @@
 }
 ## END of SUB
 
+
+=head2 METHOD checkHmdbUrlEntries
+
+ ## Description : check a list of HMDB_IDs by testing what is the status of their uri (HTTP 200 or not)
+ ## Input : $urlRoot, $entries
+ ## Output : $validEntries
+ ## Usage : my ( $validEntries ) = checkHmdbUrlEntries ( $entries ) ;
+
+=cut
+## START of SUB
+sub checkHmdbUrlEntries {
+    ## Retrieve Values
+    my $self = shift ;
+    my ( $urlRoot, $clusters, $maxQuery ) = @_;
+    my ( @ValidResults, @validFeature ) = ( (), () ) ;
+    
+    foreach my $resultsByMass (@{$clusters}) {
+ my $currentQuery = 0 ;
+     foreach my $feature (@{$resultsByMass}) {
+
+ if ($feature->{ENTRY_ENTRY_ID}) {
+
+ my $url = $urlRoot.$feature->{ENTRY_ENTRY_ID} ;
+      if ( get($url)) {
+      $currentQuery ++ ;
+      if ($currentQuery > $maxQuery) {
+     last ;
+     }
+     else {
+      push (@validFeature, $feature) ;
+#      print "Url is valid ($url) - - add to final results\n" ;
+     }
+      }
+      else {
+#      print "Url is NOT valid ($url) - - Deleting to final results\n" ;
+      next ;
+      }
+ }
+     } # END FOREACH FEATURE
+     my @tmp = @validFeature ;
+     push (@ValidResults, \@tmp) ;
+     @validFeature = () ;
+    } # END FOREACH RESULTS
+    
+    return (\@ValidResults) ;
+}
+### END of SUB
+
+
 =head2 METHOD testMatchesFromHmdbWithUA
 
  ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test02.html
--- a/test-data/out_test02.html Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test02.html Fri Nov 20 17:29:18 2020 +0000
b
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"/><!-- JavaScript --><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><!-- HeadRows--><table id="detail_table" class="detail"><col style="width:30px;"><!-- Ids (m/z)--><col style="width:30px;"><!-- Mass (m/z)--><col style="width:120px;"><!-- Met name--><col style="width:50px;"><!-- Cpd ID--><col style="width:40px;"><!-- formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- adduct --><col style="width:20px;"><!-- adduct type--><col style="width:60px;"><!-- adduct mw--><col style="width:50px;"><!-- delta--><col style="width:120px;"><!-- INCHI--><col style="width:20;"><!-- logP--><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(2+)</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">N-Nitrosodimethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031419" target="_blank" class="btn">HMDB0031419</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">Acetohydrazide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060428" target="_blank" class="btn"'..b'ass="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Trimethylamine N-oxide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000925" target="_blank" class="btn">HMDB0000925</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</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">1-Amino-propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0012136" target="_blank" class="btn">HMDB0012136</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</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">Methyloxirane</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031558" target="_blank" class="btn">HMDB0031558</a></td><td class="ca">C3H6O</td><td class="ca">58.041864814</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">3-aminopropan-1-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0140038" target="_blank" class="btn">HMDB0140038</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</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">N-monomethylethanolamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0142449" target="_blank" class="btn">HMDB0142449</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">Trimethylamine N-oxide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000925" target="_blank" class="btn">HMDB0000925</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</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">1-Amino-propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0012136" target="_blank" class="btn">HMDB0012136</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</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">Methyloxirane</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031558" target="_blank" class="btn">HMDB0031558</a></td><td class="ca">C3H6O</td><td class="ca">58.041864814</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 &copy; 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'
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test02.tabular
--- a/test-data/out_test02.tabular Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test02.tabular Fri Nov 20 17:29:18 2020 +0000
[
@@ -1,7 +1,7 @@
 id mz rt hmdb(delta::name::mz::formula::adduct::id)
-1 7.02080998 49.38210915 68::[Beryllium(2+)]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387
-2 75.05547146 0.658528069 "2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetohydrazide]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Glycinamid]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[3-Guanidinopropanoic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222"
-3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[Tert-butanol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB0006006"
-4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Glycinate]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501"
-5 76.07584477 50.51249853 "2::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-Methylethanolamine]::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::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
-6 76.07593168 0.149308136 "3::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-Methylethanolamine]::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::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
+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"
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test02.txt
--- a/test-data/out_test02.txt Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test02.txt Fri Nov 20 17:29:18 2020 +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(2+)] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387
+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 [Acetohydrazide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428
-mz_00002 75.05547146 2 [Glycinamid] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472
+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 [3-Guanidinopropanoic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222
+mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222
 mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250
-mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221
+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 [Tert-butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456
-mz_00003 75.08059797 2 [Isobutanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0006006
+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 [Glycinate] 74.024751953 C2H4NO2 [M+H] 76.039304 HMDB0161401
 mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239
-mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186
-mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062501
-mz_00005 76.07584477 2 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
-mz_00005 76.07584477 2 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
+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 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716
-mz_00006 76.07593168 3 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
-mz_00006 76.07593168 3 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
+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 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716
+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
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test03.html
--- a/test-data/out_test03.html Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test03.html Fri Nov 20 17:29:18 2020 +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"/><!-- JavaScript --><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><!-- HeadRows--><table id="detail_table" class="detail"><col style="width:30px;"><!-- Ids (m/z)--><col style="width:30px;"><!-- Mass (m/z)--><col style="width:120px;"><!-- Met name--><col style="width:50px;"><!-- Cpd ID--><col style="width:40px;"><!-- formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- adduct --><col style="width:20px;"><!-- adduct type--><col style="width:60px;"><!-- adduct mw--><col style="width:50px;"><!-- delta--><col style="width:120px;"><!-- INCHI--><col style="width:20;"><!-- logP--><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">"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0149376" target="_blank" class="btn">HMDB0149376</a></td><td class="ca">C19H16O14S</td><td class="ca">500.026076369</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">175.009949</td><td class="ca">0</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0149375" target="_blank" class="btn">HMDB0149375</a></td><td class="ca">C19H16O14S</td><td class="ca">500.026076369</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">175.009949</td><td class="ca">0</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"2-hydroxy-3-({5-hydroxy-3-[4-hydro'..b'5.023714</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">Dehydroascorbic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0001264" target="_blank" class="btn">HMDB0001264</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">dehydroascorbide(1-)</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062706" target="_blank" class="btn">HMDB0062706</a></td><td class="ca">C6H6O6</td><td class="ca">174.016437913</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="green"><td class="ca" >mz_00002</td><td id="2" class="ca" >238.19</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><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >420.16</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Fenvalerate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031791" target="_blank" class="btn">HMDB0031791</a></td><td class="ca">C25H22ClNO3</td><td class="ca">419.128821282</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">420.136097</td><td class="ca">57</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">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">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><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 &copy; 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'
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test03.tabular
--- a/test-data/out_test03.tabular Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test03.tabular Fri Nov 20 17:29:18 2020 +0000
[
@@ -1,31 +1,11 @@
 ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376
-mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375
-mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391
-mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392
-mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418
-mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116
-mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564
-mz_00002 238.19 4 [(S)-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_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 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148
-mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149
-mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020
-mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081
-mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
-mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078
-mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083
-mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342
-mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300
-mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193
-mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231
-mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858
-mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 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 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990
-mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993
-mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972
-mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992
+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_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_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test03.txt
--- a/test-data/out_test03.txt Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test03.txt Fri Nov 20 17:29:18 2020 +0000
[
@@ -1,31 +1,11 @@
 ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376
-mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375
-mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391
-mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392
-mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418
-mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116
-mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564
-mz_00002 238.19 4 [(S)-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_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 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148
-mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149
-mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020
-mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081
-mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
-mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078
-mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083
-mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342
-mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300
-mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193
-mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231
-mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858
-mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 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 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990
-mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993
-mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972
-mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992
+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_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_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test04.html
--- a/test-data/out_test04.html Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test04.html Fri Nov 20 17:29:18 2020 +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"/><!-- JavaScript --><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><!-- HeadRows--><table id="detail_table" class="detail"><col style="width:30px;"><!-- Ids (m/z)--><col style="width:30px;"><!-- Mass (m/z)--><col style="width:120px;"><!-- Met name--><col style="width:50px;"><!-- Cpd ID--><col style="width:40px;"><!-- formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- adduct --><col style="width:20px;"><!-- adduct type--><col style="width:60px;"><!-- adduct mw--><col style="width:50px;"><!-- delta--><col style="width:120px;"><!-- INCHI--><col style="width:20;"><!-- logP--><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">SCHEMBL300353</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0171211" target="_blank" class="btn">HMDB0171211</a></td><td class="ca">C4H8O4S</td><td class="ca">152.014329912</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.003548</td><td class="ca">37</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">[(2Z)-but-2-en-1-yloxy]sulfonic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0167141" target="_blank" class="btn">HMDB0167141</a></td><td class="ca">C4H8O4S</td><td class="ca">152.014329912</td><td class="ca">M+Na</td><'..b'7</a></td><td class="ca">C10H21N3O2</td><td class="ca">215.163376931</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">238.152595</td><td class="ca">157</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-Nonanoylglycine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0013279" target="_blank" class="btn">HMDB0013279</a></td><td class="ca">C11H21NO3</td><td class="ca">215.152143543</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">238.141362</td><td class="ca">204</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >420.16</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Simulansamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0030435" target="_blank" class="btn">HMDB0030435</a></td><td class="ca">C22H23NO6</td><td class="ca">397.152537473</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">420.141755</td><td class="ca">43</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">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><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">"(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"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062476" target="_blank" class="btn">HMDB0062476</a></td><td class="ca">C31H51NO29S</td><td class="ca">933.2267458</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.215964</td><td class="ca">36</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(3S)-3-isopropenyl-6-oxoheptanoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062370" target="_blank" class="btn">HMDB0062370</a></td><td class="ca">C31H50N7O18P3S</td><td class="ca">933.214589966</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.203808</td><td class="ca">48</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 &copy; 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'
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test04.tabular
--- a/test-data/out_test04.tabular Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test04.tabular Fri Nov 20 17:29:18 2020 +0000
[
@@ -1,24 +1,16 @@
 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 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211
-mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141
-mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694
-mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182
-mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239
-mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508
-mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202
+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_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 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604
-mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565
-mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435
-mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501
-mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327
-mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422
-mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421
-mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418
-mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423
-mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424
-mz_00005 956.25 36 [Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xyl] 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 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_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A
b
diff -r 63ba1cb240b7 -r 453fbe98925a test-data/out_test04.txt
--- a/test-data/out_test04.txt Thu Feb 14 08:36:52 2019 -0500
+++ b/test-data/out_test04.txt Fri Nov 20 17:29:18 2020 +0000
[
@@ -1,24 +1,16 @@
 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 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211
-mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141
-mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694
-mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182
-mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239
-mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508
-mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202
+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_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 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604
-mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565
-mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435
-mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501
-mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327
-mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422
-mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421
-mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418
-mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423
-mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424
-mz_00005 956.25 36 [Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xyl] 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 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_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A
b
diff -r 63ba1cb240b7 -r 453fbe98925a wsdl_hmdb.pl
--- a/wsdl_hmdb.pl Thu Feb 14 08:36:52 2019 -0500
+++ b/wsdl_hmdb.pl Fri Nov 20 17:29:18 2020 +0000
[
@@ -144,6 +144,7 @@
  foreach my $mzs ( @{$submasses} ) {
 # print Dumper $mzs ;
  my $result = undef ;
+ my $cleanedResult = undef ;
 
  my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
  my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ;
@@ -157,9 +158,16 @@
 
  sleep(1) ;
 
- ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result
- ## This previous step return results with cutoff on the number of entries returned ! 
- $results = [ @$results, @$result ] ;
+ ## hard modification with $max_query fixed at 1000 !!! Need to be refactoring
+ ## Cutof will be done in next method after URI check
+ ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, 1000) ; ## hash format result
+
+ ## This previous step return results with cutoff on the number of entries returned !
+
+ ## clean/max result by testing each HMDB_ID page in HMDB
+ ($cleanedResult) = $oHmdb->checkHmdbUrlEntries($CONF->{'HMDB_METABOCARD_URL'}, $result, $max_query ) ;
+
+ $results = [ @$results, @$cleanedResult ] ;
 
 # sleep(1) ;
  $cluster ++ ;
b
diff -r 63ba1cb240b7 -r 453fbe98925a wsdl_hmdb.xml
--- a/wsdl_hmdb.xml Thu Feb 14 08:36:52 2019 -0500
+++ b/wsdl_hmdb.xml Fri Nov 20 17:29:18 2020 +0000
b
@@ -232,6 +232,7 @@
    <param name="delta" value="0.05"/>
    <param name="mode" value="positive"/>
    <param name="maxquery" value="5"/>
+   <param name="adduct_type" value="M+H"/>
    <output name="variableMetadata2" file="out_test03.tabular"/>
    <output name="HmdbOutWeb2" file="out_test03.html"/>
    <output name="HmdbOutXlsx2" file="out_test03.txt"/>