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

Changeset 25:8f7546d0b925 (2022-07-05)
Previous changeset 24:d8e2ede293a6 (2022-05-19)
Commit message:
master branch Updating with tag :CI_COMMIT_TAG - - Fxx
modified:
Dockerfile
README.txt
lib/hmdb.pm
test-data/out_test02.html
test-data/out_test02.tabular
test-data/out_test02.txt
wsdl_hmdb.pl
wsdl_hmdb.xml
b
diff -r d8e2ede293a6 -r 8f7546d0b925 Dockerfile
--- a/Dockerfile Thu May 19 14:41:34 2022 +0000
+++ b/Dockerfile Tue Jul 05 12:39:15 2022 +0000
[
@@ -1,53 +1,39 @@
-# ref install: ubuntu 20.04
-FROM ubuntu:20.04
-
-# init var
-ARG DEBIAN_FRONTEND=noninteractive
+#FROM pfem/perlfull
+FROM python:3.8-buster
 
 # set author
-MAINTAINER Franck Giacomoni <franck.giacomoni.fr>
+LABEL maintainer="franck.giacomoni@inrae.fr"
 
-### 
-### [CONTAINER CORE FUNCTIONS]: 
-###   xxxx
-###   xxxx
-### [NOTES] 
-###   xxxx
+ENV PLANEMO_VENV_LOCATION /planemo-venv
+ENV CONDA /tmp/conda
 
-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 && \
+RUN apt-get update &&\
+    apt-get upgrade -y &&\
+    apt-get install --no-install-recommends --yes build-essential \
+     git \
+        libgl1-mesa-glx \
+        libegl1-mesa \
+        libxrandr2 \
+        libxss1 \
+        libxcursor1 \
+        libxcomposite1 \
+        libasound2 \
+        libxi6 \
+        libxtst6 \
+        python-virtualenv && \
+    pip install virtualenv && \
+    python3 -m virtualenv "$PLANEMO_VENV_LOCATION" && \
+    . "$PLANEMO_VENV_LOCATION"/bin/activate && \
+    pip install --upgrade pip setuptools && \
+    pip install planemo numpy && \
+    pip install -U planemo && \
+    #planemo conda_init --conda_prefix "$CONDA" && \
     apt-get autoremove -y && \
     apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
+    rm -rf /var/lib/apt/lists/*  && \
+    rm -rf /tmp/*  && \
+    rm -rf /var/tmp/*  && \
+    rm -rf /usr/bin/X11 ;
+    
+CMD []
\ No newline at end of file
b
diff -r d8e2ede293a6 -r 8f7546d0b925 README.txt
--- a/README.txt Thu May 19 14:41:34 2022 +0000
+++ b/README.txt Tue Jul 05 12:39:15 2022 +0000
b
@@ -1,5 +1,5 @@
 ## ****** HMDB environnemnt : ****** ##
-# version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team
+# version June 2022 M Landi / F Giacomoni - INRAE - METABOHUB - workflow4metabolomics.org core team
 
 ## --- PERL compilator / libraries : --- ##
 $ perl -v
b
diff -r d8e2ede293a6 -r 8f7546d0b925 lib/hmdb.pm
--- a/lib/hmdb.pm Thu May 19 14:41:34 2022 +0000
+++ b/lib/hmdb.pm Tue Jul 05 12:39:15 2022 +0000
[
@@ -709,10 +709,12 @@
  if ($line !~ /query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,"delta\(ppm\),",ccs_value/) {
  #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" ;
+     #if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\+|\-|\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),(\d*)/   ) {
+     if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\+|\-|\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),.*/   ) { # works on NEG AND POS results
+     print "$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") ;
+     my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9") ;
+     #my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
 
      if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
          
b
diff -r d8e2ede293a6 -r 8f7546d0b925 test-data/out_test02.html
--- a/test-data/out_test02.html Thu May 19 14:41:34 2022 +0000
+++ b/test-data/out_test02.html Tue Jul 05 12:39:15 2022 +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">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_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">O-Methylisourea</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255861" target="_blank" class="btn">HMDB0255861</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012821</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-Propyl-N-nitrosourea</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255236" target="_blank" class="btn">HMDB0255236</a></td><td class="ca">C4H9N3O2</td>'..b'NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><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">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">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="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">Propanediol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0256813" target="_blank" class="btn">HMDB0256813</a></td><td class="ca">C3H8O2</td><td class="ca">76.052429498</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">76.075129</td><td class="ca">11</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></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 d8e2ede293a6 -r 8f7546d0b925 test-data/out_test02.tabular
--- a/test-data/out_test02.tabular Thu May 19 14:41:34 2022 +0000
+++ b/test-data/out_test02.tabular Tue Jul 05 12:39:15 2022 +0000
[
@@ -1,7 +1,7 @@
 id mz rt hmdb(delta::name::mz::formula::adduct::id)
-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"
+1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387
+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 | 10::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+NH4-H2O]::HMDB0248304"
+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 | 1::[Ethanol]::46.041864814::C2H6O::[2M+H-H2O]::HMDB0000108 | 2::[Cyclopropane]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0250673 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250"
+4 76.03942694 51.23158899 "6::[Tri-hydroxymethylaminomethane]::93.042593089::C2H7NO3::[M+H-H2O]::HMDB0259134 | 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 | 6::[""2-Aminoethane-1,1,1-triol""]::93.042593089::C2H7NO3::[M+H-H2O]::HMDB0247334"
+5 76.07584477 50.51249853 "2::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 9::[Propanediol]::76.052429498::C3H8O2::[M+NH4-H2O]::HMDB0256813 | 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"
+6 76.07593168 0.149308136 "3::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 11::[Propanediol]::76.052429498::C3H8O2::[M+NH4-H2O]::HMDB0256813 | 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"
b
diff -r d8e2ede293a6 -r 8f7546d0b925 test-data/out_test02.txt
--- a/test-data/out_test02.txt Thu May 19 14:41:34 2022 +0000
+++ b/test-data/out_test02.txt Tue Jul 05 12:39:15 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 0 UNKNOWN N/A N/A N/A N/A N/A
+mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387
 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_00002 75.05547146 10 [o-Acetylhydroxylamine] 75.032028405 C2H5NO2 [M+NH4-H2O] 75.054728 HMDB0248304
 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 1 [Ethanol] 46.041864814 C2H6O [2M+H-H2O] 75.08053 HMDB0000108
 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 2 [Propylene] 42.046950192 C3H6 [M+CH3OH+H] 75.080439 HMDB0256839
+mz_00004 76.03942694 6 [Tri-hydroxymethylaminomethane] 93.042593089 C2H7NO3 [M+H-H2O] 76.039893 HMDB0259134
 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_00004 76.03942694 6 ["2-Aminoethane-1,1,1-triol"] 93.042593089 C2H7NO3 [M+H-H2O] 76.039893 HMDB0247334
 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 9 [Propanediol] 76.052429498 C3H8O2 [M+NH4-H2O] 76.075129 HMDB0256813
 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 11 [Propanediol] 76.052429498 C3H8O2 [M+NH4-H2O] 76.075129 HMDB0256813
 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
b
diff -r d8e2ede293a6 -r 8f7546d0b925 wsdl_hmdb.pl
--- a/wsdl_hmdb.pl Thu May 19 14:41:34 2022 +0000
+++ b/wsdl_hmdb.pl Tue Jul 05 12:39:15 2022 +0000
[
@@ -162,6 +162,8 @@
  ## Cutof will be done in next method after URI check
  ($result) = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, 1000) ; ## hash format result
 
+# print Dumper $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
@@ -275,7 +277,7 @@
 # Email : fgiacomoni\@inra.fr
 # Version : 1.6
 # Created : 08/07/2012
-# Updated : 23/01/2019 - 1.6
+# Updated : 22/06/2022 - 1.7.2
 USAGE :  
  wsdl_hmdb.pl  -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 
 
@@ -349,4 +351,6 @@
 
 version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal
 
+version 1.7.2 : 22/ 06 / 2022 - Fix issue with neg result parsing
+
 =cut
\ No newline at end of file
b
diff -r d8e2ede293a6 -r 8f7546d0b925 wsdl_hmdb.xml
--- a/wsdl_hmdb.xml Thu May 19 14:41:34 2022 +0000
+++ b/wsdl_hmdb.xml Tue Jul 05 12:39:15 2022 +0000
b
@@ -1,4 +1,4 @@
-<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.1">
+<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.2">
   <description>
         search by masses on HMDB v5 online LCMS bank
   </description>