--- 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