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changeset 14:625fa968d99a draft

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Master branch Updating - - Fxx
author fgiacomoni
date Thu, 10 Jan 2019 09:10:14 -0500
parents 3587cb923890
children beb9619263b0
files lib/csv.pm lib/hmdb.pm test-data/out_test01.txt test-data/out_test02.html test-data/out_test02.tabular test-data/out_test02.txt test-data/out_test03.tabular test-data/out_test03.txt wsdl_hmdb.pl wsdl_hmdb.xml
diffstat 10 files changed, 85 insertions(+), 51 deletions(-) [+]
line wrap: on
line diff
--- a/lib/csv.pm	Tue Oct 02 04:59:13 2018 -0400
+++ b/lib/csv.pm	Thu Jan 10 09:10:14 2019 -0500
@@ -194,10 +194,44 @@
     
     my $fh = undef ;
     $csv->eol ("\n"); ##  end-of-line string to add to rows
+#	$csv->quote_char(undef) ;
+    open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!";
+    
+	my $status = $csv->print ($fh, $_) for @{$rows};
+	close $fh or die "$file_name: $!";
+    
+    return(\$file_name) ;
+}
+## END of SUB
+
+
+=head2 METHOD write_csv_from_hash
+
+	## Description : write a csv file from simple hash with headers
+	## Input : $csv, $file_name, $headers, $arrayofhash
+	## Output : $csv_file
+	## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $headers, $arrayofhash ) ;
+	
+=cut
+## START of SUB
+sub write_csv_from_array_of_hash {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $csv, $file_name, $headers, $hash ) = @_ ;
+    
+    my $fh = undef ;
+    $csv->eol ("\n"); ##  end-of-line string to add to rows
 	$csv->quote_char(undef) ;
     open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!";
     
-	my $status = $csv->print ($fh, $_) for @{$rows};
+    if (defined $headers) {
+    	for my $field (@$headers) {	print $fh join('\t', $field), "\n"; } ;
+    }
+		
+	for my $row (keys %{$hash}) {
+		print $fh join('\t', map { $_, $row->{$_} } sort keys %$row), "\n";
+	}
+	
 	close $fh or die "$file_name: $!";
     
     return(\$file_name) ;
--- a/lib/hmdb.pm	Tue Oct 02 04:59:13 2018 -0400
+++ b/lib/hmdb.pm	Thu Jan 10 09:10:14 2019 -0500
@@ -195,12 +195,15 @@
     	croak "No http status is defined for the distant server" ;
     }
     else {
-    	unless ( $$status == 200 ) { 
+    	unless ( $$status == 200 ) {
     		if  ( $$status == 504 ) { croak "Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server" ; }
+    		if  ( $$status == 500 ) { croak "Internal Server Error: The HMDB server returns an unexpected internal server error" ; }
     		else {
     			## None supported http code error ##
+    			croak "Internal Server Error $$status..." ;
     		}
     	}
+    	if  ( $$status == 200 ) { print "The HMDB server returns that your request was fulfilled" ; }
     }
     
     return (1) ;
@@ -232,7 +235,7 @@
 	
 	$req->content_type('application/x-www-form-urlencoded');
 	$req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV');
-	 
+#	print Dumper $req ; 
 	my $res = $ua->request($req);
 #	print $res->as_string;
 	if ($res->is_success) {
@@ -269,26 +272,10 @@
     my %features = () ;
     
 #    print Dumper $csv ;
+#    print Dumper $masses ;
+#    print Dumper $max_query ;
     
     foreach my $line (@{$csv}) {
-    	## HMDB csv output - [DEPRECATED]...
-#    	if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) {
-#    		my @entry = split(/,/, $line) ;
-#    		
-#    		if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
-#    		
-#    		$features{ENTRY_ENTRY_ID} = $entry[1] ;
-#    		$features{ENTRY_FORMULA} = $entry[2] ;
-#    		$features{ENTRY_CPD_MZ} = $entry[3] ;
-#    		$features{ENTRY_ADDUCT} = $entry[4] ;
-#    		$features{ENTRY_ADDUCT_TYPE} = $entry[5] ;
-#    		$features{ENTRY_ADDUCT_MZ} = $entry[6] ;
-#    		$features{ENTRY_DELTA} = $entry[7] ;
-#    		
-#    		my %temp = %features ;
-#    		
-#    		push (@{$result_by_entry{$entry[0]} }, \%temp) ;
-#    	}
     	## NEW HMDB format V4.0 - dec2017
 		if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) {
     		
@@ -341,6 +328,7 @@
     	else {push (@results, [] ) ;} ;
 
     }
+    
     return(\@results) ;
 }
 ## END of SUB
@@ -1030,7 +1018,8 @@
     my $self = shift ;
     my ( $csv_file, $rows ) = @_ ;
 
-    my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
+#    my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
+	my $ocsv = lib::csv::new() ;
 	my $csv = $ocsv->get_csv_object("\t") ;
 	$ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
     
@@ -1053,7 +1042,7 @@
     my ( $masses, $ids, $results, $file,  ) = @_ ;
 
     open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
-    print CSV "ID\tQuery(Da)\tDelta\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
+    print CSV "ID\tQuery(Da)\tDelta(ppm)\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
     	
     my $i = 0 ;
     	
--- a/test-data/out_test01.txt	Tue Oct 02 04:59:13 2018 -0400
+++ b/test-data/out_test01.txt	Thu Jan 10 09:10:14 2019 -0500
@@ -1,4 +1,4 @@
-ID	Query(Da)	Delta	Metabolite_Name	Cpd_MW(Da)	Formula	Adduct	Adduct_MW(Da)	HMDB_ID
+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_00002	75.05547146	0	UNKNOWN	N/A	N/A	N/A	N/A	N/A
 mz_00003	75.08059797	0	UNKNOWN	N/A	N/A	N/A	N/A	N/A
--- a/test-data/out_test02.html	Tue Oct 02 04:59:13 2018 -0400
+++ b/test-data/out_test02.html	Thu Jan 10 09:10:14 2019 -0500
@@ -1,1 +1,1 @@
-<?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</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">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">InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3</td><td class="ca">-0.53</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Acetylhydrazine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060428" target="_blank" class="btn">HMDB0060428</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">InChI=1S/C2H6N2O/c1-2(5)4-3/h3H2,1H3,(H,4,5)</td><td class="ca">-0.78</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">InChI=1S/C2H6N2O/c3-1-2(4)5/h1,3H2,(H2,4,5)</td><td class="ca">-2.49</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Creatine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000064" target="_blank" class="btn">HMDB0000064</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476547</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)</td><td class="ca">-1.59</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Beta-Guanidinopropionic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0013222" target="_blank" class="btn">HMDB0013222</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476547</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">InChI=1S/C4H9N3O2/c5-4(6)7-2-1-3(8)9/h1-2H2,(H,8,9)(H4,5,6,7)</td><td class="ca">-1.70</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >75.08059797</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/HMDB0155221" target="_blank" class="btn">HMDB0155221</a></td><td class="ca">H4O7P2</td><td class="ca">177.943225506</td><td class="ca">M+H+2Na</td><td class="ca">+</td><td class="ca">75.080599</td><td class="ca">0</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">1-Butanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0004327" target="_blank" class="btn">HMDB0004327</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">InChI=1S/C4H10O/c1-2-3-4-5/h5H,2-4H2,1H3</td><td class="ca">0.84</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/HMDB0062103" target="_blank" class="btn">HMDB0062103</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062326" target="_blank" class="btn">HMDB0062326</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">InChI=1S/C4H10O/c1-3-5-4-2/h3-4H2,1-2H3</td><td class="ca">1.12</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-Butanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0011469" target="_blank" class="btn">HMDB0011469</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">InChI=1S/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H3</td><td class="ca">0.66</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >76.03942694</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">L-Aspartic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000191" target="_blank" class="btn">HMDB0000191</a></td><td class="ca">C4H7NO4</td><td class="ca">133.037507717</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1</td><td class="ca">-3.52</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Ethyl nitrite</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031239" target="_blank" class="btn">HMDB0031239</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028409</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H3</td><td class="ca">0.42</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">1-deoxy-1-(N6-lysino)-D-fructose</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062186" target="_blank" class="btn">HMDB0062186</a></td><td class="ca">C4H7NO4</td><td class="ca">133.037507709</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)</td><td class="ca">-3.52</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Glycine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000123" target="_blank" class="btn">HMDB0000123</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028409</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)</td><td class="ca">-3.34</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Acetohydroxamic Acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0014691" target="_blank" class="btn">HMDB0014691</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028409</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)</td><td class="ca">-1.46</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >76.07584477</td><td class="ca" colspan="10"></td></tr><tr class="white"><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">2</td><td class="ca">InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2</td><td class="ca">-1.01</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">InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3</td><td class="ca">-1.03</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-(methylamino)ethan-1-ol</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">2</td><td class="ca">InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3</td><td class="ca">-1.05</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">InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3</td><td class="ca">-2.01</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Allyl alcohol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031652" target="_blank" class="btn">HMDB0031652</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">InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2</td><td class="ca">-0.03</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">InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2</td><td class="ca">-1.01</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">InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3</td><td class="ca">-1.03</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-(methylamino)ethan-1-ol</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">InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3</td><td class="ca">-1.05</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">InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3</td><td class="ca">-2.01</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Allyl alcohol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031652" target="_blank" class="btn">HMDB0031652</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">InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2</td><td class="ca">-0.03</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>
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+<?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</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">InChI=1S/Be/q+2</td><td class="ca">NA</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">InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3</td><td class="ca">-0.53</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Acetylhydrazine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060428" target="_blank" class="btn">HMDB0060428</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">InChI=1S/C2H6N2O/c1-2(5)4-3/h3H2,1H3,(H,4,5)</td><td class="ca">-0.78</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">InChI=1S/C2H6N2O/c3-1-2(4)5/h1,3H2,(H2,4,5)</td><td class="ca">-2.49</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Creatine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000064" target="_blank" class="btn">HMDB0000064</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476547</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)</td><td class="ca">-1.59</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Beta-Guanidinopropionic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0013222" target="_blank" class="btn">HMDB0013222</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476547</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">InChI=1S/C4H9N3O2/c5-4(6)7-2-1-3(8)9/h1-2H2,(H,8,9)(H4,5,6,7)</td><td class="ca">-1.70</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >75.08059797</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Pyrophosphate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000250" target="_blank" class="btn">HMDB0000250</a></td><td class="ca">H4O7P2</td><td class="ca">177.943225506</td><td class="ca">M+H+2Na</td><td class="ca">+</td><td class="ca">75.080599</td><td class="ca">0</td><td class="ca">InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0155221" target="_blank" class="btn">HMDB0155221</a></td><td class="ca">H4O7P2</td><td class="ca">177.943225506</td><td class="ca">M+H+2Na</td><td class="ca">+</td><td class="ca">75.080599</td><td class="ca">0</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">1-Butanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0004327" target="_blank" class="btn">HMDB0004327</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">InChI=1S/C4H10O/c1-2-3-4-5/h5H,2-4H2,1H3</td><td class="ca">0.84</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-Methylpropan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031456" target="_blank" class="btn">HMDB0031456</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">InChI=1S/C4H10O/c1-4(2,3)5/h5H,1-3H3</td><td class="ca">0.70</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Isobutanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0006006" target="_blank" class="btn">HMDB0006006</a></td><td class="ca">C4H10O</td><td class="ca">74.073164942</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.080441</td><td class="ca">2</td><td class="ca">InChI=1S/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H3</td><td class="ca">0.60</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >76.03942694</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">L-Aspartic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000191" target="_blank" class="btn">HMDB0000191</a></td><td class="ca">C4H7NO4</td><td class="ca">133.037507717</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1</td><td class="ca">-3.52</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/HMDB0161401" target="_blank" class="btn">HMDB0161401</a></td><td class="ca">C2H4NO2</td><td class="ca">74.024751953</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Ethyl nitrite</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031239" target="_blank" class="btn">HMDB0031239</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028409</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H3</td><td class="ca">0.42</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">1-deoxy-1-(N6-lysino)-D-fructose</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062186" target="_blank" class="btn">HMDB0062186</a></td><td class="ca">C4H7NO4</td><td class="ca">133.037507709</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)</td><td class="ca">-3.52</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-acetyl-seryl-aspartate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062501" target="_blank" class="btn">HMDB0062501</a></td><td class="ca">C4H7NO4</td><td class="ca">133.037507709</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)</td><td class="ca">-3.52</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >76.07584477</td><td class="ca" colspan="10"></td></tr><tr class="white"><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">2</td><td class="ca">InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2</td><td class="ca">-1.01</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-(methylamino)ethan-1-ol</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">2</td><td class="ca">InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3</td><td class="ca">-1.05</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">InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3</td><td class="ca">-2.01</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">InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3</td><td class="ca">-1.03</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/HMDB0168716" target="_blank" class="btn">HMDB0168716</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">2</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >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">InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2</td><td class="ca">-1.01</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-(methylamino)ethan-1-ol</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">InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3</td><td class="ca">-1.05</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">InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3</td><td class="ca">-2.01</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">InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3</td><td class="ca">-1.03</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/HMDB0168716" target="_blank" class="btn">HMDB0168716</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">NA</td><td class="ca">NA</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row">  <div class="col-lg-12"><p>Copyright &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>
\ No newline at end of file
--- a/test-data/out_test02.tabular	Tue Oct 02 04:59:13 2018 -0400
+++ b/test-data/out_test02.tabular	Thu Jan 10 09:10:14 2019 -0500
@@ -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::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 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::[UNKNOWN]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[UNKNOWN]::74.073164942::C4H10O::[M+H]::HMDB0062103 | 2::[1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether]::74.073164942::C4H10O::[M+H]::HMDB0062326 | 2::[2-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0011469
-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::[1-deoxy-1-(N6-lysino)-D-fructose]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 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::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB0031652
-6	76.07593168	0.149308136	3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB0031652
+1	7.02080998	49.38210915	68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387
+2	75.05547146	0.658528069	"2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 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 | 0::[UNKNOWN]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[2-Methylpropan-2-ol]::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::[UNKNOWN]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[1-deoxy-1-(N6-lysino)-D-fructose]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[N-acetyl-seryl-aspartate]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501"
+5	76.07584477	50.51249853	"2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[2-(methylamino)ethan-1-ol]::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::[UNKNOWN]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
+6	76.07593168	0.149308136	"3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[2-(methylamino)ethan-1-ol]::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::[UNKNOWN]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
--- a/test-data/out_test02.txt	Tue Oct 02 04:59:13 2018 -0400
+++ b/test-data/out_test02.txt	Thu Jan 10 09:10:14 2019 -0500
@@ -1,27 +1,27 @@
-ID	Query(Da)	Delta	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
+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	[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	[glycinamide]	74.048012824	C2H6N2O	[M+H]	75.055289	HMDB0062472
 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_00003	75.08059797	0	[Pyrophosphate]	177.943225506	H4O7P2	[M+H+2Na]	75.080599	HMDB0000250
 mz_00003	75.08059797	0	[UNKNOWN]	177.943225506	H4O7P2	[M+H+2Na]	75.080599	HMDB0155221
 mz_00003	75.08059797	2	[1-Butanol]	74.073164942	C4H10O	[M+H]	75.080441	HMDB0004327
-mz_00003	75.08059797	2	[UNKNOWN]	74.073164942	C4H10O	[M+H]	75.080441	HMDB0062103
-mz_00003	75.08059797	2	[1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether]	74.073164942	C4H10O	[M+H]	75.080441	HMDB0062326
-mz_00003	75.08059797	2	[2-Butanol]	74.073164942	C4H10O	[M+H]	75.080441	HMDB0011469
+mz_00003	75.08059797	2	[2-Methylpropan-2-ol]	74.073164942	C4H10O	[M+H]	75.080441	HMDB0031456
+mz_00003	75.08059797	2	[Isobutanol]	74.073164942	C4H10O	[M+H]	75.080441	HMDB0006006
 mz_00004	76.03942694	2	[L-Aspartic acid]	133.037507717	C4H7NO4	[M+H+NH4]	76.039304	HMDB0000191
+mz_00004	76.03942694	2	[UNKNOWN]	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	[1-deoxy-1-(N6-lysino)-D-fructose]	133.037507709	C4H7NO4	[M+H+NH4]	76.039304	HMDB0062186
-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_00004	76.03942694	2	[N-acetyl-seryl-aspartate]	133.037507709	C4H7NO4	[M+H+NH4]	76.039304	HMDB0062501
 mz_00005	76.07584477	2	[3-aminopropan-1-ol]	75.068413915	C3H9NO	[M+H]	76.07569	HMDB0140038
-mz_00005	76.07584477	2	[1-Amino-propan-2-ol]	75.068413915	C3H9NO	[M+H]	76.07569	HMDB0012136
 mz_00005	76.07584477	2	[2-(methylamino)ethan-1-ol]	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	[Allyl alcohol]	58.041864814	C3H6O	[M+NH4]	76.075688	HMDB0031652
+mz_00005	76.07584477	2	[1-Amino-propan-2-ol]	75.068413915	C3H9NO	[M+H]	76.07569	HMDB0012136
+mz_00005	76.07584477	2	[UNKNOWN]	133.110278727	C6H15NO2	[M+H+NH4]	76.075689	HMDB0168716
 mz_00006	76.07593168	3	[3-aminopropan-1-ol]	75.068413915	C3H9NO	[M+H]	76.07569	HMDB0140038
-mz_00006	76.07593168	3	[1-Amino-propan-2-ol]	75.068413915	C3H9NO	[M+H]	76.07569	HMDB0012136
 mz_00006	76.07593168	3	[2-(methylamino)ethan-1-ol]	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	[Allyl alcohol]	58.041864814	C3H6O	[M+NH4]	76.075688	HMDB0031652
+mz_00006	76.07593168	3	[1-Amino-propan-2-ol]	75.068413915	C3H9NO	[M+H]	76.07569	HMDB0012136
+mz_00006	76.07593168	3	[UNKNOWN]	133.110278727	C6H15NO2	[M+H+NH4]	76.075689	HMDB0168716
--- a/test-data/out_test03.tabular	Tue Oct 02 04:59:13 2018 -0400
+++ b/test-data/out_test03.tabular	Thu Jan 10 09:10:14 2019 -0500
@@ -1,4 +1,4 @@
-ID	Query(Da)	Delta	Metabolite_Name	Cpd_MW(Da)	Formula	Adduct	Adduct_MW(Da)	HMDB_ID
+ID	Query(Da)	Delta(ppm)	Metabolite_Name	Cpd_MW(Da)	Formula	Adduct	Adduct_MW(Da)	HMDB_ID
 mz_00001	175.01	0	[UNKNOWN]	500.026076369	C19H16O14S	[M+2H+Na]	175.009949	HMDB0149376
 mz_00001	175.01	0	[UNKNOWN]	500.026076369	C19H16O14S	[M+2H+Na]	175.009949	HMDB0149375
 mz_00001	175.01	0	[UNKNOWN]	500.026076369	C19H16O14S	[M+2H+Na]	175.009949	HMDB0149391
--- a/test-data/out_test03.txt	Tue Oct 02 04:59:13 2018 -0400
+++ b/test-data/out_test03.txt	Thu Jan 10 09:10:14 2019 -0500
@@ -1,4 +1,4 @@
-ID	Query(Da)	Delta	Metabolite_Name	Cpd_MW(Da)	Formula	Adduct	Adduct_MW(Da)	HMDB_ID
+ID	Query(Da)	Delta(ppm)	Metabolite_Name	Cpd_MW(Da)	Formula	Adduct	Adduct_MW(Da)	HMDB_ID
 mz_00001	175.01	0	[UNKNOWN]	500.026076369	C19H16O14S	[M+2H+Na]	175.009949	HMDB0149376
 mz_00001	175.01	0	[UNKNOWN]	500.026076369	C19H16O14S	[M+2H+Na]	175.009949	HMDB0149375
 mz_00001	175.01	0	[UNKNOWN]	500.026076369	C19H16O14S	[M+2H+Na]	175.009949	HMDB0149391
--- a/wsdl_hmdb.pl	Tue Oct 02 04:59:13 2018 -0400
+++ b/wsdl_hmdb.pl	Thu Jan 10 09:10:14 2019 -0500
@@ -127,9 +127,16 @@
 		my $result = undef ;
 		my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
 		$hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
+		
+#		print Dumper $hmdb_pages ;
+		
+		sleep(2) ;
+		
 		($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 ] ;
+		
+		sleep(2) ;
 	}
 	
 	## foreach metabolite get its own metabocard
--- a/wsdl_hmdb.xml	Tue Oct 02 04:59:13 2018 -0400
+++ b/wsdl_hmdb.xml	Thu Jan 10 09:10:14 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="wsdl_hmdb" name="HMDB MS search" version="2018-10-01">
   <description>
-        search by masses on HMDB online bank
+        search by masses on HMDB online LCMS bank
   </description>
   
   <requirements>
@@ -92,9 +92,9 @@
   </outputs>
   
   <tests>
-<!-- 
+	<!--test 01 no result - fake-mzrt-input-with-id -->
+  	<!--
   	<test>
-  		<!~~test 01 no result - fake-mzrt-input-with-id ~~>
   		<param name="choice" value="YES"/>
   		<param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
   		<param name="header_choice" value="yes"/>
@@ -107,8 +107,10 @@
   		<output name="HmdbOutWeb" file="out_test01.html"/>
   		<output name="HmdbOutXlsx" file="out_test01.txt"/>
   	</test>
+  	-->
+  	<!--test 02 : some results - with-mzrt-input-with-id file-->
+  	<!--
   	<test>
-  		<!~~test 02 : some results - with-mzrt-input-with-id file~~>
   		<param name="choice" value="YES"/>
   		<param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
   		<param name="header_choice" value="yes"/>
@@ -121,9 +123,9 @@
   		<output name="HmdbOutWeb" file="out_test02.html"/>
   		<output name="HmdbOutXlsx" file="out_test02.txt"/>
   	</test>
- -->
+ 	-->
+ 	<!--test 03 : some results - with-mz list in manual mass mode-->
   	<test>
-  		<!--test 03 : some results - with-mz list in manual mass mode-->
   		<param name="choice" value="NO"/>
   		<param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
   		<param name="delta" value="0.05"/>
@@ -147,6 +149,7 @@
 
 **Please cite** If you use this tool, please add the following reference
   | Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013.
+  | Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018.
 
 
 ---------------------------------------------------
@@ -271,7 +274,7 @@
 
 .. class:: warningmark
 
-And their "W4M courses 2015":
+And their "W4M courses 2018":
  | Using Galaxy4Metabolomics - W4M table format for Galaxy
  | Annotation Banks - Annotation  
 	
@@ -280,5 +283,6 @@
 	<!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
   <citations>
     <citation type="doi">10.1093/nar/gks1065</citation>
+    <citation type="doi">10.1093/nar/gkx1089</citation>
   </citations>
 </tool>
\ No newline at end of file