hmdb_ms_search: wsdl_hmdb.pl annotate

annotate wsdl_hmdb.pl @ 23:2d8a310e86ce draft

Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx

author	fgiacomoni
date	Thu, 19 May 2022 13:43:09 +0000
parents	453fbe98925a
children	d8e2ede293a6

rev	line source
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1 #!perl
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	2
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	3 ## script : wsdl_hmdb.pl
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	4 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	5 # Included modules and versions
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	6 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	7 ## Perl modules
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	8 use strict ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	9 use warnings ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	10 use Carp qw (cluck croak carp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	11
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	12 use Data::Dumper ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	13 use Getopt::Long ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	14 use POSIX ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	15 use FindBin ; ## Permet de localisez le repertoire du script perl d'origine
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	16
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	17 ## Specific Modules (Home made...)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	18 use lib $FindBin::Bin ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	19 my $binPath = $FindBin::Bin ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	20 use lib::hmdb qw( :ALL ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	21 ## PFEM Perl Modules
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	22 use lib::conf qw( :ALL ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	23 use lib::csv qw( :ALL ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	24
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	25 ## Initialized values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	26 my ( $help ) = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	27 my ( $mass ) = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	28 my ( $masses_file, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	29 my $max_query = undef ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	30 my ( $adductType, $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef, undef ) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	31 my $advancedFeatures = 0 ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	32 my $VERBOSE = ( 3 ) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	33
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	34
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	35 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	36 # Manage EXCEPTIONS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	37 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	38
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	39 &GetOptions ( "h" => \$help, # HELP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	40 "mass:s" => \$mass, ## option : one masse
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	41 "masses:s" => \$masses_file, ## option : path to the input
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	42 "header_choice:s" => \$header_choice, ## Presence or not of header in tabular file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	43 "nblineheader:i" => \$nbline_header, ## numbre of header line present in file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	44 "colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	45 "adduct_type:s" => \$adductType, ## A list of selected adducts
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	46 "delta:f" => \$delta,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	47 "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	48 "maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 )
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	49 "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results )
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	50 "output_html\|v:s" => \$out_html, ## option : path to the results view (output2)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	51 "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	52 #"advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	53 "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	54 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	55
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	56 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	57 # EXCEPTIONS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	58 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	59 $help and &help ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	60
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	61 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	62 # MAIN SCRIPT
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	63 #=============================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	64
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	65 print "* * * The hmdb client program is launched: * * *\n" if ($VERBOSE>1) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	66
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	67 ## -------------- Conf file ------------------------ :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	68 my ( $CONF ) = ( undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	69 foreach my $conf ( <$binPath/*.cfg> ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	70 my $oConf = lib::conf::new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	71 $CONF = $oConf->as_conf($conf) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	72 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	73
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	74 ## -------------- HTML template file ------------------------ :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	75 foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	76
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	77 if (!defined $max_query) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	78 $max_query = $CONF->{'HMDB_MAX_QUERY'} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	79 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	80
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	81
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	82 ## --------------- Global parameters ---------------- :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	83 my ( $ids, $masses, $results ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	84 my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	85 my $metabocard_features = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	86 my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	87
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	88 print "\twith $search_condition\n" if ($VERBOSE>1) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	89
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	90 ## $adductType
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	91 if (defined $adductType ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	92 print "\twith Adducts: $adductType\n" if ($VERBOSE>1) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	93 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	94
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	95
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	96 ## --------------- retrieve input data -------------- :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	97
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	98 ## manage only one mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	99 if ( ( defined $mass ) and ( $mass ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	100 my @masses = split(" ", $mass);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	101 $masses = \@masses ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	102 for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	103 } ## END IF
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	104 ## manage csv file containing list of masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	105 elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	106 ## parse all csv for later : output csv build
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	107 my $ocsv_input = lib::csv->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	108 my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	109 $complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	110
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	111 ## parse masses and set ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	112 my $ocsv = lib::csv->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	113 my $csv = $ocsv->get_csv_object( "\t" ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	114 if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	115 $masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	116 my $nbmz = @$masses ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	117 for (my $i=1 ; $i<=$nbmz+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	118 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	119 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	120 warn "[warning] Input data are missing : none mass or file of masses\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	121 &help ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	122 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	123 #print Dumper $masses ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	124
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	125 ## ---------------- launch queries -------------------- :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	126
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	127 if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	128 ## prepare masses list and execute query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	129 my $oHmdb = lib::hmdb::new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	130 my $hmdb_pages = undef ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	131 my $status = undef ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	132 my ($hmdb_ids, $idsNumber) = (undef, 0) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	133
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	134 $results = [] ; # prepare arrays ref
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	135 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	136
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	137 print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	138
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	139 ## get the hmdb server status by a test query - continuous queries or kill script.
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	140 $status = $oHmdb->testMatchesFromHmdb5WithUA() ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	141 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	142
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	143 my $cluster = 1 ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	144 foreach my $mzs ( @{$submasses} ) {
10 4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 8 diff changeset	145 # print Dumper $mzs ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	146 my $result = undef ;
22 453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	147 my $cleanedResult = undef ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	148
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	149 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	150 my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	151
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 19 diff changeset	152 print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 10 diff changeset	153
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	154 ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	155 print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 10 diff changeset	156
16 8b2fbd449ffd Master branch Updating - - Fxx fgiacomoni parents: 15 diff changeset	157 # print Dumper $hmdb_pages ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	158
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	159 sleep(1) ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 10 diff changeset	160
22 453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	161 ## hard modification with $max_query fixed at 1000 !!! Need to be refactoring
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	162 ## Cutof will be done in next method after URI check
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	163 ($result) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_pages, $mzs, 1000) ; ## hash format result
22 453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	164
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	165 ## This previous step return results with cutoff on the number of entries returned !
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	166
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	167 ## clean/max result by testing each HMDB_ID page in HMDB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	168 ($cleanedResult) = $oHmdb->checkHmdbUrlEntries($CONF->{'HMDB_METABOCARD_URL'}, $result, $max_query ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	169
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	170 $results = [ @$results, @$cleanedResult ] ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 10 diff changeset	171
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	172 # sleep(1) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	173 $cluster ++ ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	174 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	175
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	176 ## Add more information of each found metabolite (1 for extra or 0 by default)
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	177 if ($advancedFeatures > 0) {
19 f8c8a990688a Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	178
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	179 ## foreach metabolite get its own metabocard
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	180 ($hmdb_ids, $idsNumber) = $oHmdb->get_unik_ids_from_results($results) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	181
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	182 print "\tComplementary annotation: asking for $idsNumber metabocards\n" if ($VERBOSE>1) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	183
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	184 # $hmdb_ids->{'HMDB03125'} = 1 ,
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	185 $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	186 # print Dumper $results ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	187 # print Dumper $hmdb_ids ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	188 # print Dumper $metabocard_features ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	189 ## Map metabocards with results (add supplementary data)
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	190 if ( ( defined $results ) and ( defined $metabocard_features ) ) {
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	191 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	192 }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	193 }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	194 else {
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	195 print "\tNo complementary annotation asked\n" if ($VERBOSE>1) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	196 ## Fill with msg not asked advanced annotation
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	197 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, undef) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	198 }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	199
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	200 ## Uses N mz and theirs entries per page (see config file).
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	201 # how many pages you need with your input mz list?
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	202 $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	203
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	204 # print Dumper $results ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	205 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	206 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	207 croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	208 } ## end ELSE
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	209
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	210 ## -------------- Produce HTML/CSV output ------------------ :
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	211 print "\n\tProducing html and tabular outputs\n" if ($VERBOSE>1) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	212
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	213 if ( ( defined $out_html ) and ( defined $results ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	214 my $oHtml = lib::hmdb::new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	215 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	216 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	217 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	218
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	219 print Dumper $tbody_object ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	220
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	221
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	222 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'}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	223
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	224 } ## END IF
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	225 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	226 warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	227 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	228
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	229 if ( ( defined $out_tab ) and ( defined $results ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	230 # produce a csv based on METLIN format
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	231 my $ocsv = lib::hmdb::new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	232 if (defined $masses_file) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	233 my $lm_matrix = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	234 if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	235 # $lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	236 $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	237 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	238 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	239 elsif ( ( $header_choice eq 'no' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	240 # $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	241 $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	242 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	243 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	244 $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	245 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	246 elsif (defined $mass) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	247 $ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	248 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	249 } ## END IF
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	250 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	251 warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	252 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	253
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	254 ## Write XLS like format
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	255 if ( ( defined $out_xls ) and ( defined $results ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	256 my $ocsv = lib::hmdb::new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	257 $ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	258 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	259
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	260 print "\n* * * The hmdb client program ended * * *\n" if ($VERBOSE>1) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	261
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	262 #====================================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	263 # Help subroutine called with -h option
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	264 # number of arguments : 0
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	265 # Argument(s) :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	266 # Return : 1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	267 #====================================================================================
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	268 sub help {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	269 print STDERR "
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	270 help of wsdl_hmdb
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	271
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	272 # 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.
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	273 # Input : accurate mz or list of accurate masses
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	274 # Author : Franck Giacomoni and Marion Landi
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	275 # Email : fgiacomoni\@inra.fr
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	276 # Version : 1.6
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	277 # Created : 08/07/2012
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	278 # Updated : 23/01/2019 - 1.6
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	279 USAGE :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	280 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]
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	281
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	282 or
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	283 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]
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	284 -delta [mz delta] -mode [molecular species: positive\|negative\|neutral] -output [output tabular file] -view [output html file]
49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	285 -advancedFeatures [Default 0, set to 1 for advanced features as logp, inchi, ...]
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	286
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	287 or
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	288 wsdl_hmdb.pl -h for help
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	289
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	290 ";
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	291 exit(1);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	292 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	293
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	294 ## END of script - F Giacomoni
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	295
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	296 __END__
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	297
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	298 =head1 NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	299
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	300 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.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	301
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	302 =head1 USAGE
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	303
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	304 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]
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	305
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	306 or
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	307 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]
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	308 -delta [mz delta] -mode [molecular species: positive\|negative\|neutral] -output [output tabular file] -view [output html file]
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	309
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	310 =head1 SYNOPSIS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	311
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	312 This script manages batch queries on HMDB server (v5.0).
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	313
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	314 =head1 DESCRIPTION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	315
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	316 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.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	317
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	318 =over 4
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	319
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	320 =item B<function01>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	321
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	322 =item B<function02>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	323
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	324 =back
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	325
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	326 =head1 AUTHOR
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	327
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	328 Franck Giacomoni E<lt>franck.giacomoni@inra.frE<gt>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	329
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	330 =head1 LICENSE
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	331
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	332 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	333
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	334 =head1 VERSION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	335
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	336 version 1.0 : 06 / 06 / 2013
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	337
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	338 version 1.2 : 27 / 01 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	339
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	340 version 1.3 : 19 / 11 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	341
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	342 version 1.4 : 21 / 01 / 2016 - a clean version for community
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	343
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	344 version 1.5 : 19 / 01 / 2018 - modify parser to match HMDB V4.0 formats
49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	345
49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 16 diff changeset	346 version 1.6 : 23 / 01 / 2019 - Manage UA http error and advanced feature from hmdb.
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	347
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	348 version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	349
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	350 version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	351
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	352 =cut

Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate wsdl_hmdb.pl @ 23:2d8a310e86ce draft