--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wsdl_hmdb.pl	Wed Nov 23 09:31:50 2016 -0500
@@ -0,0 +1,287 @@
+#!perl
+
+## script  : wsdl_hmdb.pl
+#=============================================================================
+#                              Included modules and versions
+#=============================================================================
+## Perl modules
+use strict ;
+use warnings ;
+use Carp qw (cluck croak carp) ;
+
+use Data::Dumper ;
+use Getopt::Long ;
+use POSIX ;
+use FindBin ; ## Permet de localisez le repertoire du script perl d'origine
+
+## Specific Modules (Home made...)
+use lib $FindBin::Bin ;
+my $binPath = $FindBin::Bin ;
+use lib::hmdb qw( :ALL ) ;
+## PFEM Perl Modules
+use lib::conf  qw( :ALL ) ;
+use lib::csv  qw( :ALL ) ;
+
+## Initialized values
+my ( $help ) = undef ;
+my ( $mass ) = undef ;
+my ( $masses_file, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ;
+my $max_query = undef ;
+my ( $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef ) ;
+
+
+#=============================================================================
+#                                Manage EXCEPTIONS
+#=============================================================================
+
+&GetOptions ( 	"h"					=> \$help,				# HELP
+				"mass:s"			=> \$mass,				## option : one masse
+				"masses:s"			=> \$masses_file,		## option : path to the input
+				"header_choice:s"	=> \$header_choice,		## Presence or not of header in tabular file
+				"nblineheader:i"	=> \$nbline_header,		## numbre of header line present in file
+				"colfactor:i"		=> \$col_mass,			## Column id for retrieve formula list in tabular file
+				"delta:f"			=> \$delta,
+				"mode:s"			=> \$molecular_species,	## Molecular species (positive/negative/neutral)
+				"maxquery:i"		=> \$max_query, 		## Maximum query return (default is 20 entries by query // min 1 & max 50 )
+				"output_tabular:s"	=> \$out_tab,			## option : path to the ouput (tabular : input+results )
+				"output_html|v:s"	=> \$out_html,			## option : path to the results view (output2)
+				"output_xlsx:s"		=> \$out_xls,			## option : path to the xls-like format output
+            ) ;
+
+#=============================================================================
+#                                EXCEPTIONS
+#=============================================================================
+$help and &help ;
+
+#=============================================================================
+#                                MAIN SCRIPT
+#=============================================================================
+
+
+## -------------- Conf file ------------------------ :
+my ( $CONF ) = ( undef ) ;
+foreach my $conf ( <$binPath/*.cfg> ) {
+	my $oConf = lib::conf::new() ;
+	$CONF = $oConf->as_conf($conf) ;
+}
+
+## -------------- HTML template file ------------------------ :
+foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; }
+
+if (!defined $max_query) {
+	$max_query = $CONF->{'HMDB_MAX_QUERY'} ;
+}
+
+
+## --------------- Global parameters ---------------- :
+my ( $ids, $masses, $results ) = ( undef, undef, undef ) ;
+my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ;
+my $metabocard_features = undef ;
+my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ;
+
+## --------------- retrieve input data -------------- :
+
+## manage only one mass
+if ( ( defined $mass ) and ( $mass ne '' ) ) {
+	my @masses = split(" ", $mass);
+	$masses = \@masses ;
+	for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
+} ## END IF
+## manage csv file containing list of masses
+elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) {
+	## parse all csv for later : output csv build
+	my $ocsv_input  = lib::csv->new() ;
+	my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
+	$complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ;
+	
+	## parse masses and set ids
+	my $ocsv = lib::csv->new() ;
+	my $csv = $ocsv->get_csv_object( "\t" ) ;
+	if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ;	}
+	$masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv
+	my $nbmz = @$masses ;
+	for (my $i=1 ; $i<=$nbmz+1 ; $i++){ 	push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
+}
+else {
+	warn "[warning] Input data are missing : none mass or file of masses\n" ;
+	&help ;
+}
+#print Dumper $masses ;
+## ---------------- launch queries -------------------- :
+
+if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) {
+	## prepare masses list and execute query
+	my $oHmdb = lib::hmdb::new() ;
+	my $hmdb_pages = undef ;
+	my $hmdb_ids = undef ;
+	
+	$results = [] ; # prepare arrays ref
+	my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;
+	
+	## get the hmdb server status by a test query - continuous queries or kill script.
+	my $status = $oHmdb->test_matches_from_hmdb_ua() ;
+	$oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
+
+	foreach my $mzs ( @{$submasses} ) {
+		
+		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, $molecular_species) ;
+		($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 ] ;
+	}
+	
+	## foreach metabolite get its own metabocard
+	$hmdb_ids = $oHmdb->get_unik_ids_from_results($results) ;
+#	$hmdb_ids->{'HMDB03125'} = 1 ,
+	$metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying
+	
+	## Map metabocards with results (add supplementary data)
+	
+#	print Dumper $results ;
+#	print Dumper $hmdb_ids ;
+#	print Dumper $metabocard_features ;
+
+	if ( ( defined $results ) and ( defined $metabocard_features ) ) {
+		$results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;
+	}
+
+	## Uses N mz and theirs entries per page (see config file).
+	# how many pages you need with your input mz list?
+	$nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} )  ;
+	
+#	print Dumper $results ;
+}
+else {
+	croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ;
+} ## end ELSE
+
+## -------------- Produce HTML/CSV output ------------------ :
+
+if ( ( defined $out_html ) and ( defined $results ) ) {
+	my $oHtml = lib::hmdb::new() ;
+	my ($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) ;
+	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
+else {
+	warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ;
+}
+
+if ( ( defined $out_tab ) and ( defined $results ) ) {
+	# produce a csv based on METLIN format
+	my $ocsv = lib::hmdb::new() ;
+	if (defined $masses_file) {
+		my $lm_matrix = undef ;
+		if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) {
+#			$lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ;
+			$lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ;
+			$lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ;
+		}
+		elsif ( ( $header_choice eq 'no' ) ) {
+#			$lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ;
+			$lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ;
+			$lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ;
+		}
+		$ocsv->write_csv_skel(\$out_tab, $lm_matrix) ;
+	}
+	elsif (defined $mass) {
+		$ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ;
+	}
+} ## END IF
+else {
+	warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ;
+}
+
+## Write XLS like format
+if ( ( defined $out_xls ) and ( defined $results ) ) {
+	my $ocsv = lib::hmdb::new() ;
+	$ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ;
+}
+
+
+#====================================================================================
+# Help subroutine called with -h option
+# number of arguments : 0
+# Argument(s)        :
+# Return           : 1
+#====================================================================================
+sub help {
+	print STDERR "
+help of wsdl_hmdb
+
+# wsdl_hmdb is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
+# Input : formula or list of formula
+# Author : Franck Giacomoni and Marion Landi
+# Email : fgiacomoni\@clermont.inra.fr
+# Version : 1.4
+# Created : 08/07/2012
+# Updated : 21/01/2016
+USAGE :		 
+		wsdl_hmdb.pl 	-mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 
+		
+		or 
+		wsdl_hmdb.pl 	-masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n]
+						-delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 
+						
+		or 
+		wsdl_hmdb.pl 	-h for help
+		
+		";
+	exit(1);
+}
+
+## END of script - F Giacomoni 
+
+__END__
+
+=head1 NAME
+
+ wsdl_hmdb.pl -- script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
+
+=head1 USAGE
+
+	wsdl_hmdb.pl 	-mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 
+		
+	or 
+	wsdl_hmdb.pl 	-masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n]
+					-delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 
+
+=head1 SYNOPSIS
+
+This script manages batch queries on HMDB server. 
+
+=head1 DESCRIPTION
+
+This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
+
+=over 4
+
+=item B<function01>
+
+=item B<function02>
+
+=back
+
+=head1 AUTHOR
+
+Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
+
+=head1 LICENSE
+
+This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
+
+=head1 VERSION
+
+version 1.0 : 06 / 06 / 2013
+
+version 1.2 : 27 / 01 / 2014
+
+version 1.3 : 19 / 11 / 2014
+
+version 1.4 : 21 / 01 / 2016 - a clean version for community
+
+=cut
\ No newline at end of file