# HG changeset patch
# User fgiacomoni
# Date 1652967789 0
# Node ID 2d8a310e86ceb33c6fb6bdd7e4e4b33e96707445
# Parent  453fbe98925ac2043f50328f6fdef8bfff92d9cd
 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx

diff -r 453fbe98925a -r 2d8a310e86ce Dockerfile
diff -r 453fbe98925a -r 2d8a310e86ce README.md
diff -r 453fbe98925a -r 2d8a310e86ce README.txt
diff -r 453fbe98925a -r 2d8a310e86ce conf_hmdb.cfg
diff -r 453fbe98925a -r 2d8a310e86ce hmdb.tmpl
diff -r 453fbe98925a -r 2d8a310e86ce lib/conf.pm
diff -r 453fbe98925a -r 2d8a310e86ce lib/csv.pm
diff -r 453fbe98925a -r 2d8a310e86ce lib/hmdb.pm
--- a/lib/hmdb.pm	Fri Nov 20 17:29:18 2020 +0000
+++ b/lib/hmdb.pm	Thu May 19 13:43:09 2022 +0000
@@ -21,8 +21,8 @@
 
 our $VERSION = "1.0";
 our @ISA = qw(Exporter);
-our @EXPORT = qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass );
-our %EXPORT_TAGS = ( ALL => [qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] );
+our @EXPORT = qw( parseHmdb5CSVResults getMatchesFromHmdb5WithUA map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass );
+our %EXPORT_TAGS = ( ALL => [qw( parseHmdb5CSVResults getMatchesFromHmdb5WithUA map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] );
 
 =head1 NAME
 
@@ -273,7 +273,7 @@
 
 =head2 METHOD testMatchesFromHmdbWithUA
 
-	## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.
+	## Description : [DEPRECATED] test a single query with tests parameters on hmdb - get the status of the complete server infra.
 	## Input : none
 	## Output : $status_line
 	## Usage : my ( $status_line ) = testMatchesFromHmdbWithUA( ) ;
@@ -288,12 +288,14 @@
     #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
 
 	my $mech = WWW::Mechanize->new(
-		agent => 'wonderbot for W4M 1.01',
-		autocheck => 1,	
+#		agent => 'wonderbot for W4M 1.01',
+		agent => 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.14; rv:93.0) Gecko/20100101 Firefox/93.0' ,
+		autocheck => 0,
 	);
 	
 	my $statusGetLine = 0 ;
 	my $statusPostLine = 0 ;
+	my $csrftoken = undef ;
 	
 	#receiving cookies and authentication token (CFRS)
 	my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
@@ -302,13 +304,23 @@
 	if ($statusGetLine == 200 ) {
 		die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
 		unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
-		my $csrftoken = $1;
-#		print "\nTOKEN: $csrftoken\n" ;
+		$csrftoken = $1;
+		print "\nTOKEN: $csrftoken\n" ;
 		$mech->add_header("X-CSRFToken", $csrftoken);
+		$mech->add_header('Host', 'specdb.wishartlab.com');
 		$mech->add_header('Connection', 'keep-alive');
+		$mech->add_header('Upgrade-Insecure-Requests', '1');
 		$mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
-		$mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
-		$mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
+		$mech->add_header('Accept-Language', 'en-US,en;q=0.5');
+		$mech->add_header('Accept-Encoding', 'gzip, deflate');
+#		$mech->add_header('Content-Length', "300");
+		$mech->add_header('Origin', 'null');
+		$mech->add_header('DNT', '1');
+		$mech->add_header('Referer', 'https://hmdb.ca/spectra/ms/search');
+#		$mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
+		$mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8');
+		
+		
 	}
 	
 	## POST test
@@ -318,13 +330,15 @@
 		# Fix a limit at 3 tries...
 		if ($top < 4) {
 			print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
-			$mech->post(
-				"http://specdb.wishartlab.com/ms/search.csv",
-		    	Content => 'utf8=TRUE&mode=positive&adduct_type=M%2BH%202M%2BH&query_masses=125.0089&tolerance=0.001&database=HMDB&commit=Download Results As CSV'
-			);
-			
+			eval {
+				$mech->post(
+					"http://specdb.wishartlab.com/ms/search.csv",
+			    	Content => 'utf8=TRUE&authenticity_token='.$csrftoken.'&mode=positive&adduct_type=M%2BH%202M%2BH&query_masses=125.0089&tolerance=0.001&database=HMDB&commit=Download Results As CSV'
+				);
+			} ;
 #		print Dumper $mech ;
 			$statusPostLine = $mech->status() ;
+			print "Status: $statusPostLine" ;
 		}
 		else {
 			last ;
@@ -336,7 +350,82 @@
 ## END of SUB
 
 
+=head2 METHOD testMatchesFromHmdb5WithUA
 
+	## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra (API V5.0 compliant).
+	## Input : none
+	## Output : $status_line
+	## Usage : my ( $status_line ) = testMatchesFromHmdb5WithUA( ) ;
+	
+=cut
+## START of SUB
+sub testMatchesFromHmdb5WithUA {
+	## Retrieve Values
+    my $self = shift ;
+    
+my $mech = WWW::Mechanize->new(
+		agent => 'wonderbot for W4M 3.0',
+		autocheck => 1,
+		timeout => 2400,
+	);
+	
+	my $statusGetLine = 0 ;
+	my $statusPostLine = 0 ;
+	
+	#receiving cookies and authentication token (CFRS)
+	my $reqInit = $mech->get("https://www.hmdb.ca/spectra/ms/search");
+	$statusGetLine = $mech->status() ;
+	
+	if ($statusGetLine == 200 ) {
+		die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
+		unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
+		my $csrftoken = $1;
+#		print "\nTOKEN: $csrftoken\n" ;
+		$mech->add_header("X-CSRFToken", $csrftoken);
+		$mech->add_header('Connection', 'keep-alive');
+		$mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
+		$mech->add_header('Referer', 'https://www.hmdb.ca/spectra/ms/search');
+		$mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
+	}
+	
+	
+	## POST test
+	my $top = 1 ;
+	while ($statusPostLine != 200 ) {
+		
+		# Fix a limit at 3 tries...
+		if ($top < 4) {
+			print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
+			eval {
+				my $res = $mech->get(
+					'https://hmdb.ca/spectra/ms/generate_csv.csv?'
+					.'results%5Baction%5D=search'
+					.'&results%5Badduct_type%5D%5B%5D=M%2BH%202M%2BH'
+					#.'&results%5Bauthenticity_token%5D='
+					.'&results%5Bccs_predictors%5D='
+					.'&results%5Bccs_tolerance%5D='
+					.'&results%5Bcommit%5D=Search'
+					.'&results%5Bcontroller%5D=specdb%2Fms'
+					.'&results%5Bms_search_ion_mode%5D=positive'
+					.'&results%5Bquery_masses%5D=125.0089'
+					.'&results%5Btolerance%5D=0.001'
+					.'&results%5Btolerance_units%5D=Da'
+					.'&results%5Butf8%5D=%E2%9C%93'
+				
+				);
+			} ;
+#		print Dumper $mech ;
+			$statusPostLine = $mech->status() ;
+			print "Status: $statusPostLine" ;
+		}
+		else {
+			last ;
+		}
+		$top++ ;
+	}## End While
+	return (\$statusPostLine) ;
+}
+## END of SUB
 
 =head2 METHOD check_state_from_hmdb_ua
 
@@ -353,7 +442,7 @@
     my ($status) = @_ ;
     
     if (!defined $$status) {
-    	croak "No http status is defined for the distant server" ;
+    	croak "No https status is defined for the distant server" ;
     }
     else {
     	unless ( $$status == 200 ) {
@@ -389,6 +478,10 @@
     my $self = shift ;
     my ( $masses, $delta, $mode ) = @_ ;
     
+    ## Added May, 2022
+    warn "[DEPRECATED Methode] method get_matches_from_hmdb_ua is deprecated and not compatible with HMDB 4.0" ;
+    return ([], 500) ;
+    
     my @page = () ;
 
 	my $ua = LWP::UserAgent->new( keep_alive => 10 );
@@ -443,6 +536,10 @@
     my $self = shift ;
     my ( $masses, $delta, $mode, $adducts ) = @_ ;
     
+    ## Added May, 2022
+    warn "[DEPRECATED Methode] method getMatchesFromHmdbWithUA is deprecated and not compatible with HMDB 5.0" ;
+    return ([], 500) ;
+    
     my @page = () ;
     
     #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
@@ -501,10 +598,185 @@
 }
 ## END of SUB
 
+=head2 METHOD getMatchesFromHmdb5WithUA
+
+	## Description : HMDB v5.0 querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
+	## Input : $mass, $delta, $mode, adducts
+	## Output : $results
+	## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
+	
+=cut
+## START of SUB
+sub getMatchesFromHmdb5WithUA {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $masses, $delta, $mode, $adducts ) = @_ ;
+    
+    my @page = () ;
+    
+    #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
+
+	my $mech = WWW::Mechanize->new(
+		agent => 'wonderbot for W4M 3.0',
+		autocheck => 1,
+		timeout => 2400,
+	);
+	
+	my $statusGetLine = 0 ;
+	my $statusPostLine = 0 ;
+	
+	#receiving cookies and authentication token (CFRS)
+	my $reqInit = $mech->get("https://www.hmdb.ca/spectra/ms/search");
+	$statusGetLine = $mech->status() ;
+	
+	if ($statusGetLine == 200 ) {
+		die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
+		unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
+		my $csrftoken = $1;
+#		print "\nTOKEN: $csrftoken\n" ;
+		$mech->add_header("X-CSRFToken", $csrftoken);
+		$mech->add_header('Connection', 'keep-alive');
+		$mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
+		$mech->add_header('Referer', 'https://www.hmdb.ca/spectra/ms/search');
+		$mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
+	}
+	## adduct format is adduct_type=M%2BH%202M%2BH
+	
+	if ( (!defined $adducts) or ( $adducts eq '')  ) {
+		$adducts = 'Unknown' ;
+	}
+		
+	my $res = $mech->get(
+		'https://hmdb.ca/spectra/ms/generate_csv.csv?'
+		.'results%5Baction%5D=search'
+		.'&results%5Badduct_type%5D%5B%5D='.$adducts
+		#.'&results%5Bauthenticity_token%5D='
+		.'&results%5Bccs_predictors%5D='
+		.'&results%5Bccs_tolerance%5D='
+		.'&results%5Bcommit%5D=Search'
+		.'&results%5Bcontroller%5D=specdb%2Fms'
+		.'&results%5Bms_search_ion_mode%5D='.$mode
+		.'&results%5Bquery_masses%5D='.$masses
+		.'&results%5Btolerance%5D='.$delta
+		.'&results%5Btolerance_units%5D=Da'
+		.'&results%5Butf8%5D=%E2%9C%93'
+	
+	);
+	$statusGetLine = $mech->status() ;
+	
+	if ($mech->success) {
+		@page = split ( /\n/, $res->decoded_content ) ;
+		$statusPostLine = 'OK' ;
+	}
+	else {
+		$statusPostLine = $mech->status() ;
+		warn "\t[HMDB service issue !! the server returned a $statusPostLine HTTP error]" ;
+	}
+	
+#	print Dumper $res->decoded_content ;
+
+	return (\@page, $statusPostLine) ;
+}
+## END of SUB
+
+
+=head2 METHOD parseHmdb5CSVResults
+
+	## Description : parse the csv results and get data - API 5.0 compliant
+	## Input : $csv
+	## Output : $results
+	## Usage : my ( $results ) = parseHmdb5CSVResults( $csv ) ;
+	
+=cut
+## START of SUB
+sub parseHmdb5CSVResults {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $csv, $masses, $max_query ) = @_ ;
+    
+    my $test = 0 ;
+    my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ;
+    
+    my %result_by_entry = () ;
+    my %features = () ;
+    
+#    print Dumper $csv ;
+#    print Dumper $masses ;
+#    print Dumper $max_query ;
+    
+    foreach my $line (@{$csv}) {
+    	## NEW HMDB format V5.0 - May2022
+		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|n\/a|\s+]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/  ) {
+    			my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
+
+    			if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
+    			    		
+	    		$features{ENTRY_ENTRY_ID} = $entry[1] ;
+	    		$features{ENTRY_ENTRY_NAME} = $entry[2] ;
+	    		$features{ENTRY_FORMULA} = $entry[3] ;
+	    		$features{ENTRY_CPD_MZ} = $entry[4] ;
+	    		$features{ENTRY_ADDUCT} = $entry[5] ;
+	    		$features{ENTRY_ADDUCT_TYPE} = $entry[6] ;
+	    		$features{ENTRY_ADDUCT_MZ} = $entry[7] ;
+	    		$features{ENTRY_DELTA} = $entry[8] ;
+	    		
+	    		my %temp = %features ;
+	    		push (@{$result_by_entry{$entry[0]} }, \%temp) ;
+    		}
+#    		elsif ($line =~ /(\d+\.\d+)/) { #
+#    			## 288.082286511284,HMDB0002255,R-Methylmalonyl-CoA, C01213 ,C25H40N7O19P3S,867.131252359,M-3H,-,288.036475,159
+#    			## 283.108004472276,"Bicyclo_3,1,1heptane-2,3-diol,2,6,6_trimethyl","2,3-Pinanediol",n/a,C10H18O2,170.13067982,M+TFA-H,-,283.116266,29
+#    			## 174.034120330029,HMDB0011723,2-Methylhippuric acid,	 C01586,C10H11NO3,193.073893223,M-H20-H,-,174.055503,123
+#    			## 193.139160745841,HMDB0012109,"7-[(1R,2R,3R,5S)-3,5-Dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid", C06475,C20H36O7,388.246103506,M-2H,-,193.115776,121
+#    			## 214.018826827064,HMDB0011723,2-Methylhippuric acid,	 C01586,C10H11NO3,193.073893223,M+Na-2H,-,214.048559,139
+#    		}
+#    		else {
+#    			
+#    			warn "The parsed line ($line) does not match your pattern\n " ;
+#    		}
+    	}
+    	else {
+    		print "Header detected...Parsing is starting...\n" ;
+    		next ;
+    	}
+    } ## end foreach
+    
+    ## manage per query_mzs (keep query masses order by array)
+    my @results = () ;
+    foreach (@{$masses}) {
+    	if ($result_by_entry{$_}) { 
+    	
+    		## cut all entries > $max_query	- all entries were already sorted...by hmdb
+    		my @temp_entries = @{$result_by_entry{$_}} ;
+    		my @temp_cut = () ;
+    		my $current_query = 0 ;
+    		foreach (@temp_entries) {
+    			$current_query ++ ;
+    			if ($current_query > $max_query) {
+    				last ;
+    			}
+    			else {
+    				push (@temp_cut, $_) ;
+    			}	
+    		}
+    		push (@results, \@temp_cut) ; 
+    	}
+    	else { push (@results, [] ) ; } ;
+
+    }
+    return(\@results) ;
+}
+## END of SUB
+
 
 =head2 METHOD parse_hmdb_csv_results
 
-	## Description : parse the csv results and get data
+	## Description : [DEPRECATED] parse the csv results and get data
 	## Input : $csv
 	## Output : $results
 	## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
diff -r 453fbe98925a -r 2d8a310e86ce static/images/hmdb.png
diff -r 453fbe98925a -r 2d8a310e86ce t/hmdb_managerTest.pl
--- a/t/hmdb_managerTest.pl	Fri Nov 20 17:29:18 2020 +0000
+++ b/t/hmdb_managerTest.pl	Thu May 19 13:43:09 2022 +0000
@@ -43,68 +43,36 @@
 		['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ), 
 		'175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 
 		'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying');
-		
+	
 	print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++;
-	is_deeply( get_matches_from_hmdb_uaTest(
+	is_deeply( getMatchesFromHmdb5WithUATest(
 		'175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'),
 		[
-          'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
-#          '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
-#          '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
-#          '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
-#          '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
-#          '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
-#          '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
-#          '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
-			## Update format - 2018-01-19... HMDB V04
-#			'175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
-#			'175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
-#			'175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
-#			'175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
-#			'175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
-#			'420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
-#			'420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
-			## Update results - 2018-09-20... HMDBv4
-			#'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
-          '175.01,HMDB0149376,"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
-          '175.01,HMDB0149375,"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
-          '175.01,HMDB0149419,"2-{[5,8-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
-          '175.01,HMDB0149418,"2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
-          '175.01,HMDB0149392,"2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
-          '175.01,HMDB0149391,"2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0',
-          '175.01,HMDB0000257,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
-          '175.01,HMDB0060293,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
-          '175.01,HMDB0141391,{4-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
-          '175.01,HMDB0141389,{3-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
-          '175.01,HMDB0135622,{4-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
-          '175.01,HMDB0135448,{3-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
-          '175.01,HMDB0240280,Methanesulfonic acid,C11145,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4',
-          '175.01,HMDB0003745,Coenzyme m,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
-          '175.01,HMDB0142159,[2-hydroxy-2-(2-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142160,[2-hydroxy-1-(2-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142162,"[3-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142166,"[4-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142164,[2-hydroxy-1-(3-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142163,[2-hydroxy-2-(3-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142167,[2-hydroxy-2-(4-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0142168,[2-hydroxy-1-(4-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0129951,"{3-[2-(3,5-dihydroxyphenyl)ethyl]phenyl}oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
-          '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
-          '175.01,HMDB0033657,"11,15-Dihydroxy-6,8,20-trioxapentacyclo[10.8.0.0²,⁹.0³,⁷.0¹⁴,¹⁹]icosa-1(12),2(9),4,10,14,16,18-heptaen-13-one",C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
-          '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)-2H-furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
-          '175.01,HMDB0155176,5-Hydroxy-6-hydrouracil,n/a,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6',
-          '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
-          '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
-          '420.16,HMDB0160148,"6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
-          '420.16,HMDB0160149,"6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
-          '420.16,HMDB0165020,"6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
-          '420.16,HMDB0175397,"6-{[3-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2',
-          '420.16,HMDB0184353,"6-[(4-carboxy-3,3-dimethylbutanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2'
+          'query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value',
+          '175.01,HMDB0259477,"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine",C10H18N2O3S3,310.04795597,M+H+K,+,175.009195,5,',
+          '175.01,HMDB0258038,9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid,C15H12O5S,304.04054466,M+2Na,+,175.00949,3,',
+          '175.01,HMDB0257737,"4,5-Dihydroxy-3-methyl-1H-imidazol-2-one",C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
+          '175.01,HMDB0240502,Dihydroresveratrol 4\'-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
+          '175.01,HMDB0240500,Dihydroresveratrol 3-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
+          '175.01,HMDB0246744,"5-Amino-1,3,4-thiadiazole-2-thiol",C2H3N3S2,132.976839457,M+ACN+H,+,175.010662,4,',
+          '175.01,HMDB0252977,Phosphoaminophosphonic acid-guanylate ester,C10H17N6O13P3,522.006645625,M+3H,+,175.009491,3,',
+          '175.01,HMDB0246800,5-Hydroxy-1-methylhydantoin,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
+          '175.01,HMDB0258677,Tafamidis,C14H7Cl2NO3,306.980298509,M+ACN+2H,+,175.010699,4,',
+          '175.01,HMDB0240280,Mesylate,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4,',
+          '175.01,HMDB0000257,Thiosulfate,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1,',
+          '175.01,HMDB0035230,Aurantricholide B,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
+          '175.01,HMDB0033657,De-O-methylsterigmatocystin,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
+          '175.01,HMDB0003745,Mesna,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4,',
+          '420.16,HMDB0250452,Core oligosaccharide,C27H48O24,756.253552426,M+2ACN+2H,+,420.160599,1,',
+          '420.16,HMDB0245742,"N-(6,8-Difluoro-2-methyl-4-quinolinyl)-N\'-[4-(dimethylamino)phenyl]urea",C19H18F2N4O,356.144867542,M+ACN+Na,+,420.160633,2,',
+          '420.16,HMDB0256144,Pazopanib,C21H23N7O2S,437.163393705,M+H-H2O,+,420.160694,2,',
+          '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,',
+          '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,'
         ],
-		'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb');
+		'Method \'getMatchesFromHmdb5WithUA\' works again (API v5.0 compatible) with a well-formated string of mzs and return a complete csv from hmdb');
 	
 	print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++;
-	is_deeply (test_matches_from_hmdb_uaTest (), 
+	is_deeply (testMatchesFromHmdb5WithUATest (), 
 		\'200', 
 		'The HMDB server is available: returns successful HTTP requests' ) ;
 		
@@ -113,147 +81,144 @@
 		1,
 		'The status 200 returns no error/warn' ) ;
 		
-	print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++;	
+	print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++;	
 	throws_ok{ check_state_from_hmdb_uaTest(\'504')} 
-		'/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/', 
+		qr/Gateway Timeout \(504\): The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server\. The Hmdb tool is stopped with error\./, 
 		'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ;
 		
-	print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
-	is_deeply ( parse_hmdb_csv_resultsTest (
+		
+	print "\n** Test $current_test parseHmdb5CSVResults (version 5.0) with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
+	is_deeply ( parseHmdb5CSVResultsTest (
 		[
-          'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
-#          '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
-#          '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
-#          '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
-#          '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
-#          '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
-#          '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
-#          '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
-			## Update format - 2018-01-19... HMDB V04
-			'175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
-			'175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
-			'175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
-			'175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
-			'175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
-			'420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
-			'420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
+		  'query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value',
+          '175.01,HMDB0259477,"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine",C10H18N2O3S3,310.04795597,M+H+K,+,175.009195,5,',
+          '175.01,HMDB0258038,9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid,C15H12O5S,304.04054466,M+2Na,+,175.00949,3,',
+          '175.01,HMDB0257737,"4,5-Dihydroxy-3-methyl-1H-imidazol-2-one",C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
+          '175.01,HMDB0240502,Dihydroresveratrol 4\'-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
+          '175.01,HMDB0240500,Dihydroresveratrol 3-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
+          '175.01,HMDB0246744,"5-Amino-1,3,4-thiadiazole-2-thiol",C2H3N3S2,132.976839457,M+ACN+H,+,175.010662,4,',
+          '175.01,HMDB0252977,Phosphoaminophosphonic acid-guanylate ester,C10H17N6O13P3,522.006645625,M+3H,+,175.009491,3,',
+          '175.01,HMDB0246800,5-Hydroxy-1-methylhydantoin,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
+          '175.01,HMDB0258677,Tafamidis,C14H7Cl2NO3,306.980298509,M+ACN+2H,+,175.010699,4,',
+          '175.01,HMDB0240280,Mesylate,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4,',
+          '175.01,HMDB0000257,Thiosulfate,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1,',
+          '175.01,HMDB0035230,Aurantricholide B,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
+          '175.01,HMDB0033657,De-O-methylsterigmatocystin,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
+          '175.01,HMDB0003745,Mesna,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4,',
+          '420.16,HMDB0250452,Core oligosaccharide,C27H48O24,756.253552426,M+2ACN+2H,+,420.160599,1,',
+          '420.16,HMDB0245742,"N-(6,8-Difluoro-2-methyl-4-quinolinyl)-N\'-[4-(dimethylamino)phenyl]urea",C19H18F2N4O,356.144867542,M+ACN+Na,+,420.160633,2,',
+          '420.16,HMDB0256144,Pazopanib,C21H23N7O2S,437.163393705,M+H-H2O,+,420.160694,2,',
+          '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,',
+          '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,'
         ],
         ['175.01', '238.19', '420.16'],
         10
 	),
 		[
           [
-            { 'ENTRY_CPD_MZ' => '113.94453531', 'ENTRY_ENTRY_ID' => 'HMDB0060293', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ADDUCT_MZ' => '175.009875', 'ENTRY_DELTA' => '1', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT' => 'M+IsoProp+H' },
-            {'ENTRY_DELTA' => '4','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+CH3OH+H','ENTRY_CPD_MZ' => '141.975835438','ENTRY_ENTRY_ID' => 'HMDB0003745','ENTRY_FORMULA' => 'C2H6O3S2','ENTRY_ADDUCT_MZ' => '175.009324'},
-            {'ENTRY_ENTRY_ID' => 'HMDB0031436','ENTRY_CPD_MZ' => '95.987885149','ENTRY_ADDUCT_MZ' => '175.009105','ENTRY_FORMULA' => 'H4O4Si','ENTRY_DELTA' => '5','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+DMSO+H'},
-            {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0033657','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT' => 'M+H+K','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '5'},
-            {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0035230','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+H+K','ENTRY_DELTA' => '5'}
+            { 'ENTRY_CPD_MZ' => '310.04795597', 'ENTRY_DELTA' => '5', 'ENTRY_FORMULA' => 'C10H18N2O3S3', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_ENTRY_NAME' => '"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine"', 'ENTRY_ENTRY_ID' => 'HMDB0259477', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009195' },
+            { 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.00949', 'ENTRY_ENTRY_ID' => 'HMDB0258038', 'ENTRY_ENTRY_NAME' => '9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid', 'ENTRY_FORMULA' => 'C15H12O5S', 'ENTRY_ADDUCT' => 'M+2Na', 'ENTRY_DELTA' => '3', 'ENTRY_CPD_MZ' => '304.04054466' },
+            { 'ENTRY_FORMULA' => 'C14H14O6S', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_ENTRY_NAME' => 'Dihydroresveratrol 4\'-sulfate', 'ENTRY_CPD_MZ' => '310.051109345', 'ENTRY_DELTA' => '4', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.010772', 'ENTRY_ENTRY_ID' => 'HMDB0240502' },
+            { 'ENTRY_ADDUCT_MZ' => '175.010772', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0240500', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_FORMULA' => 'C14H14O6S', 'ENTRY_ENTRY_NAME' => 'Dihydroresveratrol 3-sulfate', 'ENTRY_CPD_MZ' => '310.051109345', 'ENTRY_DELTA' => '4' },
+            { 'ENTRY_ENTRY_ID' => 'HMDB0246744', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.010662', 'ENTRY_CPD_MZ' => '132.976839457', 'ENTRY_DELTA' => '4', 'ENTRY_ENTRY_NAME' => '"5-Amino-1,3,4-thiadiazole-2-thiol"', 'ENTRY_FORMULA' => 'C2H3N3S2', 'ENTRY_ADDUCT' => 'M+ACN+H' },
+            { 'ENTRY_ENTRY_ID' => 'HMDB0252977', 'ENTRY_ADDUCT_MZ' => '175.009491', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_CPD_MZ' => '522.006645625', 'ENTRY_DELTA' => '3', 'ENTRY_ADDUCT' => 'M+3H', 'ENTRY_FORMULA' => 'C10H17N6O13P3', 'ENTRY_ENTRY_NAME' => 'Phosphoaminophosphonic acid-guanylate ester' },
+            { 'ENTRY_ENTRY_ID' => 'HMDB0258677', 'ENTRY_ADDUCT_MZ' => '175.010699', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_CPD_MZ' => '306.980298509', 'ENTRY_DELTA' => '4', 'ENTRY_ADDUCT' => 'M+ACN+2H', 'ENTRY_FORMULA' => 'C14H7Cl2NO3', 'ENTRY_ENTRY_NAME' => 'Tafamidis' },
+            { 'ENTRY_ENTRY_ID' => 'HMDB0240280', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009335', 'ENTRY_DELTA' => '4', 'ENTRY_CPD_MZ' => '95.988114684', 'ENTRY_FORMULA' => 'CH4O3S', 'ENTRY_ADDUCT' => 'M+DMSO+H', 'ENTRY_ENTRY_NAME' => 'Mesylate' },
+            { 'ENTRY_DELTA' => '1', 'ENTRY_CPD_MZ' => '113.94453531', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_ENTRY_NAME' => 'Thiosulfate', 'ENTRY_ENTRY_ID' => 'HMDB0000257', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009875' },
+            { 'ENTRY_DELTA' => '5', 'ENTRY_CPD_MZ' => '310.047738052', 'ENTRY_ENTRY_NAME' => 'Aurantricholide B', 'ENTRY_FORMULA' => 'C17H10O6', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_ENTRY_ID' => 'HMDB0035230', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009086' }
           ],
           [],
           [
-            {'ENTRY_FORMULA' => 'C17H17N3O4S','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ENTRY_ID' => 'HMDB0060838','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '2'},
-            {'ENTRY_DELTA' => '2','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ENTRY_ID' => 'HMDB0060836','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_FORMULA' => 'C17H17N3O4S'}
+            { 'ENTRY_ADDUCT_MZ' => '420.160599', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0250452', 'ENTRY_ADDUCT' => 'M+2ACN+2H', 'ENTRY_FORMULA' => 'C27H48O24', 'ENTRY_ENTRY_NAME' => 'Core oligosaccharide', 'ENTRY_CPD_MZ' => '756.253552426', 'ENTRY_DELTA' => '1' },
+            { 'ENTRY_CPD_MZ' => '356.144867542', 'ENTRY_DELTA' => '2', 'ENTRY_ENTRY_NAME' => '"N-(6,8-Difluoro-2-methyl-4-quinolinyl)-N\'-[4-(dimethylamino)phenyl]urea"', 'ENTRY_FORMULA' => 'C19H18F2N4O', 'ENTRY_ADDUCT' => 'M+ACN+Na', 'ENTRY_ENTRY_ID' => 'HMDB0245742', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '420.160633' },
+            { 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0060838', 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_ENTRY_NAME' => 'N-Desmethyl-p-hydroxyrosiglitazone', 'ENTRY_CPD_MZ' => '359.093976737', 'ENTRY_DELTA' => '2' },
+            { 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0060836', 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_ENTRY_NAME' => 'N-Desmethyl-O-hydroxy rosiglitazone', 'ENTRY_DELTA' => '2', 'ENTRY_CPD_MZ' => '359.093976737' }
           ]
         ],
-		'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;
-		
-	print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++;
-	is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ),
-		[ [], [], [] ],
-		'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ;
-	
-	print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list  **\n" ; $current_test++;
-	is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),
-		[],
-		'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ;
-
-	## Other example... from mz 265.0567515
-	print "\n** Test $current_test parse_hmdb_csv_results with mz 265.0567515 and the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
-	is_deeply ( parse_hmdb_csv_resultsTest (
-		[
-        'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
-		'265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2',
-		'265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
-		'265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
-		'265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
-		'265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
-		'265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3',
-		'265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
-		'265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
-		'265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
-		'265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4',
-        ],
-        ['265.0567515'],
-        5
-	),
-		[
-          [
-            {
-              'ENTRY_DELTA' => '2',
-              'ENTRY_FORMULA' => 'C5H8O2S',
-              'ENTRY_ENTRY_ID' => 'HMDB0059667',
-              'ENTRY_ADDUCT_MZ' => '265.056276',
-              'ENTRY_ADDUCT_TYPE' => '+',
-              'ENTRY_CPD_MZ' => '132.02450019',
-              'ENTRY_ADDUCT' => '2M+H'
-            },
-            {
-              'ENTRY_ADDUCT_MZ' => '265.056128',
-              'ENTRY_ENTRY_ID' => 'HMDB0038767',
-              'ENTRY_ADDUCT_TYPE' => '+',
-              'ENTRY_CPD_MZ' => '726.200729034',
-              'ENTRY_ADDUCT' => 'M+3Na',
-              'ENTRY_DELTA' => '2',
-              'ENTRY_FORMULA' => 'C32H38O19'
-            },
-            {
-              'ENTRY_DELTA' => '2',
-              'ENTRY_FORMULA' => 'C32H38O19',
-              'ENTRY_ENTRY_ID' => 'HMDB0039759',
-              'ENTRY_ADDUCT_MZ' => '265.056128',
-              'ENTRY_ADDUCT_TYPE' => '+',
-              'ENTRY_CPD_MZ' => '726.200729034',
-              'ENTRY_ADDUCT' => 'M+3Na'
-            },
-            {
-              'ENTRY_FORMULA' => 'C32H38O19',
-              'ENTRY_DELTA' => '2',
-              'ENTRY_ADDUCT_TYPE' => '+',
-              'ENTRY_ADDUCT_MZ' => '265.056128',
-              'ENTRY_ENTRY_ID' => 'HMDB0040875',
-              'ENTRY_CPD_MZ' => '726.200729034',
-              'ENTRY_ADDUCT' => 'M+3Na'
-            },
-            {
-              'ENTRY_ADDUCT_TYPE' => '+',
-              'ENTRY_ENTRY_ID' => 'HMDB0040878',
-              'ENTRY_ADDUCT_MZ' => '265.056128',
-              'ENTRY_ADDUCT' => 'M+3Na',
-              'ENTRY_CPD_MZ' => '726.200729034',
-              'ENTRY_FORMULA' => 'C32H38O19',
-              'ENTRY_DELTA' => '2'
-            }
-          ]
-        ],
-		'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;	
-		
-	
-}
+		'Method \'parseHmdb5CSVResults\' works with a well-formated csv output and returns a a well formated array' ) ;
 
 
-
-
-
-
-
-
-
+#	print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++;
+#	is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ),
+#		[ [], [], [] ],
+#		'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ;
+#	
+#	print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list  **\n" ; $current_test++;
+#	is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),
+#		[],
+#		'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ;
+#
+#	## Other example... from mz 265.0567515
+#	print "\n** Test $current_test parse_hmdb_csv_results with mz 265.0567515 and the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
+#	is_deeply ( parse_hmdb_csv_resultsTest (
+#		[
+#        'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
+#		'265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2',
+#		'265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
+#		'265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
+#		'265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
+#		'265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
+#		'265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3',
+#		'265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
+#		'265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
+#		'265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
+#		'265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4',
+#        ],
+#        ['265.0567515'],
+#        5
+#	),
+#		[
+#          [
+#            {
+#              'ENTRY_DELTA' => '2',
+#              'ENTRY_FORMULA' => 'C5H8O2S',
+#              'ENTRY_ENTRY_ID' => 'HMDB0059667',
+#              'ENTRY_ADDUCT_MZ' => '265.056276',
+#              'ENTRY_ADDUCT_TYPE' => '+',
+#              'ENTRY_CPD_MZ' => '132.02450019',
+#              'ENTRY_ADDUCT' => '2M+H'
+#            },
+#            {
+#              'ENTRY_ADDUCT_MZ' => '265.056128',
+#              'ENTRY_ENTRY_ID' => 'HMDB0038767',
+#              'ENTRY_ADDUCT_TYPE' => '+',
+#              'ENTRY_CPD_MZ' => '726.200729034',
+#              'ENTRY_ADDUCT' => 'M+3Na',
+#              'ENTRY_DELTA' => '2',
+#              'ENTRY_FORMULA' => 'C32H38O19'
+#            },
+#            {
+#              'ENTRY_DELTA' => '2',
+#              'ENTRY_FORMULA' => 'C32H38O19',
+#              'ENTRY_ENTRY_ID' => 'HMDB0039759',
+#              'ENTRY_ADDUCT_MZ' => '265.056128',
+#              'ENTRY_ADDUCT_TYPE' => '+',
+#              'ENTRY_CPD_MZ' => '726.200729034',
+#              'ENTRY_ADDUCT' => 'M+3Na'
+#            },
+#            {
+#              'ENTRY_FORMULA' => 'C32H38O19',
+#              'ENTRY_DELTA' => '2',
+#              'ENTRY_ADDUCT_TYPE' => '+',
+#              'ENTRY_ADDUCT_MZ' => '265.056128',
+#              'ENTRY_ENTRY_ID' => 'HMDB0040875',
+#              'ENTRY_CPD_MZ' => '726.200729034',
+#              'ENTRY_ADDUCT' => 'M+3Na'
+#            },
+#            {
+#              'ENTRY_ADDUCT_TYPE' => '+',
+#              'ENTRY_ENTRY_ID' => 'HMDB0040878',
+#              'ENTRY_ADDUCT_MZ' => '265.056128',
+#              'ENTRY_ADDUCT' => 'M+3Na',
+#              'ENTRY_CPD_MZ' => '726.200729034',
+#              'ENTRY_FORMULA' => 'C32H38O19',
+#              'ENTRY_DELTA' => '2'
+#            }
+#          ]
+#        ],
+#		'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;	
+#		
+#	
 
-
-
-
-
-
-
-
+}
 ## END of the script
\ No newline at end of file
diff -r 453fbe98925a -r 2d8a310e86ce t/lib/hmdbTest.pm
--- a/t/lib/hmdbTest.pm	Fri Nov 20 17:29:18 2020 +0000
+++ b/t/lib/hmdbTest.pm	Thu May 19 13:43:09 2022 +0000
@@ -8,8 +8,8 @@
 
 our $VERSION = "1.0";
 our @ISA = qw(Exporter);
-our @EXPORT = qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest);
-our %EXPORT_TAGS = ( ALL => [qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] );
+our @EXPORT = qw( testMatchesFromHmdb5WithUATest parseHmdb5CSVResultsTest getMatchesFromHmdb5WithUATest parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest);
+our %EXPORT_TAGS = ( ALL => [qw( testMatchesFromHmdb5WithUATest parseHmdb5CSVResultsTest getMatchesFromHmdb5WithUATest parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] );
 
 use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/hmdb' ;
 use lib::hmdb qw( :ALL ) ;
@@ -49,6 +49,17 @@
 	return ($hmdb_pages) ;
 }
 
+## sub
+sub getMatchesFromHmdb5WithUATest {
+	
+	my ( $hmdb_masses, $delta, $molecular_species ) = @_ ;
+	
+	my $oHmdb = lib::hmdb->new() ;
+	my ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species) ;
+	print Dumper $hmdb_pages ;
+	return ($hmdb_pages) ;
+}
+
 
 ## sub
 sub test_matches_from_hmdb_uaTest {
@@ -58,6 +69,13 @@
 	return ($status) ;
 }
 
+## sub
+sub testMatchesFromHmdb5WithUATest {
+	
+	my $oHmdb = lib::hmdb->new() ;
+	my $status = $oHmdb->testMatchesFromHmdb5WithUA() ;
+	return ($status) ;
+}
 
 ## sub
 sub check_state_from_hmdb_uaTest {
@@ -69,6 +87,15 @@
 }
 
 
+## sub
+sub parseHmdb5CSVResultsTest {
+	my ($hmdb_pages, $mzs, $max ) = @_ ;
+	
+	my $oHmdb = lib::hmdb->new() ;
+	my $result = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, $max) ; ## hash format result
+	#print Dumper $result ;
+	return($result) ;
+}
 
 ## sub
 sub parse_hmdb_csv_resultsTest {
diff -r 453fbe98925a -r 2d8a310e86ce test-data/input_test01_fake-mzrt-input-with-id.tabular
diff -r 453fbe98925a -r 2d8a310e86ce test-data/input_test02_mzrt-input-with-id.tabular
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test01.html
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test01.tabular
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test01.txt
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test02.html
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test02.tabular
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test02.txt
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test03.html
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test03.tabular
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test03.txt
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test04.html
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test04.tabular
diff -r 453fbe98925a -r 2d8a310e86ce test-data/out_test04.txt
diff -r 453fbe98925a -r 2d8a310e86ce wsdl_hmdb.pl
--- a/wsdl_hmdb.pl	Fri Nov 20 17:29:18 2020 +0000
+++ b/wsdl_hmdb.pl	Thu May 19 13:43:09 2022 +0000
@@ -49,7 +49,7 @@
 				"output_tabular:s"	=> \$out_tab,			## option : path to the ouput (tabular : input+results )
 				"output_html|v:s"	=> \$out_html,			## option : path to the results view (output2)
 				"output_xlsx:s"		=> \$out_xls,			## option : path to the xls-like format output
-				"advancedFeatures:i"=> \$advancedFeatures,	## option : set to 1 to get advanced options or 0 to get first level only.
+				#"advancedFeatures:i"=> \$advancedFeatures,	## option : set to 1 to get advanced options or 0 to get first level only.
 				"verbose:i"			=> \$VERBOSE,			## VERBOSE Of the tool
             ) ;
 
@@ -137,7 +137,7 @@
 	print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;
 	
 	## get the hmdb server status by a test query - continuous queries or kill script.
-	$status = $oHmdb->testMatchesFromHmdbWithUA() ;
+	$status = $oHmdb->testMatchesFromHmdb5WithUA() ;
 	$oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
 	
 	my $cluster = 1 ;
@@ -151,7 +151,7 @@
 		
 		print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ;
 		
-		($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ;
+		($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ;
 		print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ;
 		
 #		print Dumper $hmdb_pages ;
@@ -160,7 +160,7 @@
 		
 		## hard modification with $max_query fixed at 1000 !!! Need to be refactoring
 		## Cutof will be done in next method after URI check
-		($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, 1000) ; ## hash format result
+		($result) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result
 		
 		## This previous step return results with cutoff on the number of entries returned !
 		
@@ -215,6 +215,10 @@
 	my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
 	($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
 	($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
+	
+	print Dumper $tbody_object ;
+	
+	
 	my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ;
 	
 } ## END IF
@@ -305,7 +309,7 @@
 
 =head1 SYNOPSIS
 
-This script manages batch queries on HMDB server. 
+This script manages batch queries on HMDB server (v5.0). 
 
 =head1 DESCRIPTION
 
@@ -343,4 +347,6 @@
 
 version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements
 
+version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal
+
 =cut
\ No newline at end of file
diff -r 453fbe98925a -r 2d8a310e86ce wsdl_hmdb.xml
--- a/wsdl_hmdb.xml	Fri Nov 20 17:29:18 2020 +0000
+++ b/wsdl_hmdb.xml	Thu May 19 13:43:09 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.1">
+<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.0">
   <description>
         search by masses on HMDB online LCMS bank
   </description>
@@ -243,7 +243,7 @@
 
 .. class:: infomark
 
-**Authors** Marion Landi and Franck Giacomoni
+**Authors** Marion Landi, Yann Guitton and Franck Giacomoni
 
 ---------------------------------------------------
 
@@ -252,6 +252,7 @@
 **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.
+  | Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022.
 
 
 ---------------------------------------------------
@@ -376,7 +377,7 @@
 
 .. class:: warningmark
 
-And their "W4M courses 2018":
+And their "W4M courses 2021":
  | Using Galaxy4Metabolomics - W4M table format for Galaxy
  | Annotation Banks - Annotation  
 	
@@ -386,5 +387,6 @@
   <citations>
     <citation type="doi">10.1093/nar/gks1065</citation>
     <citation type="doi">10.1093/nar/gkx1089</citation>
+    <citation type="doi">10.1093/nar/gkab1062</citation>
   </citations>
 </tool>
\ No newline at end of file