hmdb_ms_search: lib/hmdb.pm annotate

annotate lib/hmdb.pm @ 22:453fbe98925a draft

" master branch Updating with tag :CI_COMMIT_TAG - - Fxx"

author	fgiacomoni
date	Fri, 20 Nov 2020 17:29:18 +0000
parents	63ba1cb240b7
children	2d8a310e86ce

rev	line source
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1 package lib::hmdb ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	2
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	3 use strict;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	4 use warnings ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	5 use Exporter ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	6 use Carp ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	7
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	8 use LWP::Simple;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	9 use LWP::UserAgent;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	10 use WWW::Mechanize qw();
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	11 use URI::URL;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	12 use SOAP::Lite;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	13 use Encode qw(encode_utf8);
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	14 use HTML::Template ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	15 use XML::Twig ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	16 use Text::CSV ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	17
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	18 use Data::Dumper ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	19
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	20 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	21
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	22 our $VERSION = "1.0";
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	23 our @ISA = qw(Exporter);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	24 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 );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	25 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 )] );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	26
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	27 =head1 NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	28
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	29 My::Module - An example module
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	30
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	31 =head1 SYNOPSIS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	32
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	33 use My::Module;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	34 my $object = My::Module->new();
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	35 print $object->as_string;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	36
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	37 =head1 DESCRIPTION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	38
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	39 This module does not really exist, it
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	40 was made for the sole purpose of
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	41 demonstrating how POD works.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	42
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	43 =head1 METHODS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	44
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	45 Methods are :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	46
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	47 =head2 METHOD new
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	48
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	49 ## Description : new
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	50 ## Input : $self
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	51 ## Ouput : bless $self ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	52 ## Usage : new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	53
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	54 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	55
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	56 sub new {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	57 ## Variables
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	58 my $self={};
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	59 bless($self) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	60 return $self ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	61 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	62 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	63
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	64
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	65 =head2 METHOD extract_sub_mz_lists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	66
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	67 ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	68 ## Input : $HMDB_LIMITS, $masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	69 ## Output : $sublists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	70 ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	71
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	72 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	73 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	74 sub extract_sub_mz_lists {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	75 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	76 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	77 my ( $masses, $HMDB_LIMITS ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	78
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	79 my ( @sublists, @sublist ) = ( (), () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	80 my $nb_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	81 my $nb_total_mzs = scalar(@{$masses}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	82
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	83 if ($nb_total_mzs == 0) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	84 die "The provided mzs list is empty" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	85 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	86
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	87 for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	88
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	89 if ( $nb_mz < $HMDB_LIMITS ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	90 if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	91 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	92 elsif ( $nb_mz == $HMDB_LIMITS ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	93 my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	94 $current_pos-- ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	95 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	96 if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	97 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	98 return(\@sublists) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	99 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	100 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	101
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	102 =head2 METHOD prepare_multi_masses_query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	103
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	104 ## Description : Generate the adapted format of the mz list for HMDB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	105 ## Input : $masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	106 ## Output : $hmdb_masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	107 ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	108
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	109 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	110 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	111 sub prepare_multi_masses_query {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	112 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	113 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	114 my ( $masses ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	115
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	116 my $hmdb_masses = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	117 my $sep = '%0D%0A' ; ## retour chariot encode
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	118 my ($nb_masses, $i) = (0, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	119
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	120 if ( defined $masses ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	121 my @masses = @{$masses} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	122 my $nb_masses = scalar ( @masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	123 if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; }
6 7ed37640fe2a planemo upload commit 4c72059b94b27eda2c0ee89bfc5f9bf4e3425dc5 fgiacomoni parents: 4 diff changeset	124 elsif ( $nb_masses >= 700 ) { croak "Your mass list is too long : HMDB allows maximum 700 query masses per request \n" ; } ## Del it --- temporary patch
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	125
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	126 foreach my $mass (@masses) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	127
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	128 if ($i < $nb_masses) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	129 $hmdb_masses .= $mass.$sep ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	130 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	131 elsif ( $i == $nb_masses ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	132 $hmdb_masses .= $mass ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	133 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	134 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	135 last ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	136 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	137 $i ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	138 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	139 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	140 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	141 croak "No mass list found \n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	142 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	143 return($hmdb_masses, $nb_masses) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	144 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	145 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	146
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	147
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	148 =head2 METHOD prepareAdductListFormat
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	149
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	150 ## Description : prepare a adduct list well formatted for https queries
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	151 ## Input : $adductString
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	152 ## Output : $formattedAdductString
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	153 ## Usage : my ( $formattedAdductString ) = prepareAdductListFormat ( $adductString ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	154
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	155 =cut
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	156 ## START of SUB
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	157 sub prepareAdductListFormat {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	158 ## Retrieve Values
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	159 my $self = shift ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	160 my ( $adductString ) = @_;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	161 my ( $formattedAdductString, $nbAdducts ) = ( undef, 0 ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	162
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	163 ## Formatting is converting [+] in %2B, [-] as - and [,] in converted space as 'M%2BH%202M%2BH' for 'M+H,2M+2H'
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	164 # print "\t$adductString ..." ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	165
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	166 if (defined $adductString) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	167
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	168 ## counting selected adducts
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	169 $nbAdducts = scalar( my @adducts = ( split (/,/, $adductString) ) ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	170
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	171 ## Converting string into http post format
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	172 $adductString =~ s/\+/%2B/g ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	173 $adductString =~ s/,/%20/g ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	174 $formattedAdductString = $adductString ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	175 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	176 else {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	177 warn "\t[WARN]the adduct type is not defined...It will set to 'Unknown'\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	178 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	179
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	180 # print "->$formattedAdductString\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	181
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	182 return ($formattedAdductString, $nbAdducts) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	183 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	184 ### END of SUB
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	185
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	186 =head2 METHOD test_matches_from_hmdb_ua DEPRECATED
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	187
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	188 ## Description : [DEPRECATED]test a single query with tests parameters on hmdb - get the status of the complete server infra.
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	189 ## Input : none
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	190 ## Output : $status_line
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	191 ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	192
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	193 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	194 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	195 sub test_matches_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	196 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	197 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	198
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	199 my @page = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	200
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	201 my $ua = new LWP::UserAgent;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	202 $ua->agent("Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:64.0) Gecko/20100101 Firefox/64.0");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	203
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	204 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	205 my $header = ['Connection' => 'keep-alive', 'Content-Type' => 'application/x-www-form-urlencoded', 'Referer' => 'http://www.hmdb.ca/spectra/ms/search', 'Accept' => 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8'];
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	206
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	207 my $req = HTTP::Request->new('POST', $url, $header);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	208 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	209
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	210 ## Query format for HMDB 4.0
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	211 #"utf8=✓&authenticity_token=K1Ys7oyMKmVNm9n8p0jiTxBlh4G4OO0cqKZYnQKDCw0pM6zmm/CiBxv+/cXhuRsVFV98LLeAMJRN5dCyhIWlAA==&query_masses=175.01 238.19 420.16 780.32 956.25 1100.45&ms_search_ion_mode=positive&adduct_type[]=Unknown&tolerance=0.05&tolerance_units=Da&commit=Search"
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	212
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	213 $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV');
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	214 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	215 my $res = $ua->request($req);
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	216
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	217 print $res->as_string;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	218 my $status_line = $res->status_line ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	219 ($status_line) = ($status_line =~ /(\d+)/);
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	220
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	221 return (\$status_line) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	222 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	223 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	224
22 453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	225
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	226 =head2 METHOD checkHmdbUrlEntries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	227
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	228 ## Description : check a list of HMDB_IDs by testing what is the status of their uri (HTTP 200 or not)
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	229 ## Input : $urlRoot, $entries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	230 ## Output : $validEntries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	231 ## Usage : my ( $validEntries ) = checkHmdbUrlEntries ( $entries ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	232
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	233 =cut
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	234 ## START of SUB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	235 sub checkHmdbUrlEntries {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	236 ## Retrieve Values
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	237 my $self = shift ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	238 my ( $urlRoot, $clusters, $maxQuery ) = @_;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	239 my ( @ValidResults, @validFeature ) = ( (), () ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	240
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	241 foreach my $resultsByMass (@{$clusters}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	242 my $currentQuery = 0 ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	243 foreach my $feature (@{$resultsByMass}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	244
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	245 if ($feature->{ENTRY_ENTRY_ID}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	246
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	247 my $url = $urlRoot.$feature->{ENTRY_ENTRY_ID} ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	248 if ( get($url)) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	249 $currentQuery ++ ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	250 if ($currentQuery > $maxQuery) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	251 last ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	252 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	253 else {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	254 push (@validFeature, $feature) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	255 # print "Url is valid ($url) - - add to final results\n" ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	256 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	257 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	258 else {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	259 # print "Url is NOT valid ($url) - - Deleting to final results\n" ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	260 next ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	261 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	262 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	263 } # END FOREACH FEATURE
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	264 my @tmp = @validFeature ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	265 push (@ValidResults, \@tmp) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	266 @validFeature = () ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	267 } # END FOREACH RESULTS
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	268
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	269 return (\@ValidResults) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	270 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	271 ### END of SUB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	272
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	273
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	274 =head2 METHOD testMatchesFromHmdbWithUA
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	275
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	276 ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	277 ## Input : none
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	278 ## Output : $status_line
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	279 ## Usage : my ( $status_line ) = testMatchesFromHmdbWithUA( ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	280
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	281 =cut
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	282 ## START of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	283 sub testMatchesFromHmdbWithUA {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	284 ## Retrieve Values
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	285 my $self = shift ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	286
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	287 my @page = () ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	288 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	289
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	290 my $mech = WWW::Mechanize->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	291 agent => 'wonderbot for W4M 1.01',
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	292 autocheck => 1,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	293 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	294
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	295 my $statusGetLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	296 my $statusPostLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	297
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	298 #receiving cookies and authentication token (CFRS)
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	299 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	300 $statusGetLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	301
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	302 if ($statusGetLine == 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	303 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	304 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	305 my $csrftoken = $1;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	306 # print "\nTOKEN: $csrftoken\n" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	307 $mech->add_header("X-CSRFToken", $csrftoken);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	308 $mech->add_header('Connection', 'keep-alive');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	309 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	310 $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	311 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	312 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	313
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	314 ## POST test
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	315 my $top = 1 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	316 while ($statusPostLine != 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	317
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	318 # Fix a limit at 3 tries...
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	319 if ($top < 4) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	320 print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	321 $mech->post(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	322 "http://specdb.wishartlab.com/ms/search.csv",
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	323 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'
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	324 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	325
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	326 # print Dumper $mech ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	327 $statusPostLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	328 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	329 else {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	330 last ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	331 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	332 $top++ ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	333 }## End While
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	334 return (\$statusPostLine) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	335 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	336 ## END of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	337
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	338
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	339
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	340
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	341 =head2 METHOD check_state_from_hmdb_ua
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	342
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	343 ## Description : check the thhp status of hmdb and kill correctly the script if necessary.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	344 ## Input : $status
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	345 ## Output : none
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	346 ## Usage : check_state_from_hmdb_ua($status) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	347
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	348 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	349 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	350 sub check_state_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	351 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	352 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	353 my ($status) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	354
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	355 if (!defined $$status) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	356 croak "No http status is defined for the distant server" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	357 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	358 else {
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	359 unless ( $$status == 200 ) {
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	360 if ( $$status == 502 ) { croak "Bad Gateway (502): The HMDB server, while acting as a gateway or proxy, received an invalid response from the upstream server. The Hmdb tool is stopped with error." ; }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	361 if ( $$status == 504 ) { croak "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." ; }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	362 if ( $$status == 500 ) { croak "Internal Server Error (500): The HMDB server returns an unexpected internal server error. The Hmdb tool is stopped with error." ; }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	363 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	364 ## None supported http code error ##
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	365 croak "Internal Server Error $$status..." ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	366 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	367 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	368 if ( $$status == 200 ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	369 print "\tThe HMDB server returns that your request (connexion test) was fulfilled\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	370 print "\tAll searches should be sent successfully to HMDB...(Set verbose to \"High\" for more information!)\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	371 }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	372 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	373
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	374 return (1) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	375 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	376 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	377
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	378 =head2 METHOD get_matches_from_hmdb_ua DEPRECATED
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	379
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	380 ## Description : [DEPRECATED]HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	381 ## Input : $mass, $delta, $mode
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	382 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	383 ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	384
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	385 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	386 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	387 sub get_matches_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	388 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	389 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	390 my ( $masses, $delta, $mode ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	391
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	392 my @page = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	393
8 97788e4bf3fc planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392-dirty fgiacomoni parents: 6 diff changeset	394 my $ua = LWP::UserAgent->new( keep_alive => 10 );
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	395 $ua->agent("Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:64.0) Gecko/20100101 Firefox/64.0");
9 c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 8 diff changeset	396 $ua->timeout(2400) ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	397
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	398 # Cookies
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	399 # my $cookie = new HTTP::Cookies( ignore_discard => 1 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	400 # $ua->cookie_jar( $cookie );
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	401
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	402 # my $req = HTTP::Request->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	403 # POST => 'http://specdb.wishartlab.com/ms/search.csv');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	404
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	405 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	406 my $header = ['Content-Type' => 'application/x-www-form-urlencoded', 'Referer' => 'http://www.hmdb.ca/spectra/ms/search', 'Accept' => 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8'];
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	407 my $data = {mode => $mode, query_masses => $masses, 'tolerance' => $delta, database => 'HMDB', commit => 'Download Results As CSV'};
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	408 my $encoded_data = encode_utf8($data);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	409
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	410 my $req = HTTP::Request->new('POST', $url, $header, $encoded_data);
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	411
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	412 # $req->content_type('application/x-www-form-urlencoded');
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	413 $req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV');
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	414 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	415 my $res = $ua->request($req);
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	416 my $status_line = undef ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	417 print $res->as_string;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	418 if ($res->is_success) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	419 @page = split ( /\n/, $res->decoded_content ) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	420 $status_line = 'OK' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	421 } else {
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	422 $status_line = $res->status_line ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	423 ($status_line) = ($status_line =~ /(\d+)/);
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 15 diff changeset	424 warn "\t[HMDB service issue !! the server returned a $status_line HTTP error]" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	425 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	426
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	427
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	428 return (\@page, $status_line) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	429 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	430 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	431
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	432 =head2 METHOD getMatchesFromHmdbWithUA
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	433
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	434 ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	435 ## Input : $mass, $delta, $mode, adducts
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	436 ## Output : $results
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	437 ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	438
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	439 =cut
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	440 ## START of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	441 sub getMatchesFromHmdbWithUA {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	442 ## Retrieve Values
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	443 my $self = shift ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	444 my ( $masses, $delta, $mode, $adducts ) = @_ ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	445
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	446 my @page = () ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	447
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	448 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	449
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	450 my $mech = WWW::Mechanize->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	451 agent => 'wonderbot for W4M 1.01',
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	452 autocheck => 1,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	453 timeout => 2400,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	454 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	455
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	456 my $statusGetLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	457 my $statusPostLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	458
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	459 #receiving cookies and authentication token (CFRS)
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	460 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	461 $statusGetLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	462
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	463 if ($statusGetLine == 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	464 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	465 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	466 my $csrftoken = $1;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	467 # print "\nTOKEN: $csrftoken\n" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	468 $mech->add_header("X-CSRFToken", $csrftoken);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	469 $mech->add_header('Connection', 'keep-alive');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	470 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	471 $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	472 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	473 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	474 ## adduct format is adduct_type=M%2BH%202M%2BH
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	475
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	476 if ( (!defined $adducts) or ( $adducts eq '') ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	477 $adducts = 'Unknown' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	478 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	479
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	480 my $res = $mech->post(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	481 "http://specdb.wishartlab.com/ms/search.csv",
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	482 Content => 'utf8=TRUE&mode='
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	483 .$mode.'&adduct_type='
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	484 .$adducts.'&query_masses='
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	485 .$masses.'&tolerance='
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	486 .$delta.'&database=HMDB&commit=Download Results As CSV'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	487 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	488
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	489 if ($mech->success) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	490 @page = split ( /\n/, $res->decoded_content ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	491 $statusPostLine = 'OK' ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	492 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	493 else {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	494 $statusPostLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	495 warn "\t[HMDB service issue !! the server returned a $statusPostLine HTTP error]" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	496 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	497
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	498 # print Dumper $res->decoded_content ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	499
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	500 return (\@page, $statusPostLine) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	501 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	502 ## END of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	503
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	504
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	505 =head2 METHOD parse_hmdb_csv_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	506
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	507 ## Description : parse the csv results and get data
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	508 ## Input : $csv
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	509 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	510 ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	511
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	512 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	513 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	514 sub parse_hmdb_csv_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	515 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	516 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	517 my ( $csv, $masses, $max_query ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	518
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	519 my $test = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	520 my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	521
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	522 my %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	523 my %features = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	524
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	525 # print Dumper $csv ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	526 # print Dumper $masses ;
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	527 # print Dumper $max_query ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	528
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	529 foreach my $line (@{$csv}) {
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	530 ## NEW HMDB format V4.0 - dec2017
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	531 if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta$ppm$/) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	532
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	533 if ( $line =~ /(\d+\.\d+),(\w+),(.),([\w\|n\/a\|\s+]+)\s,(\w+),(\d+\.\d+),(.*),(\+\|\-),(\d+\.\d+),(\d+)/ ) {
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	534 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	535
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	536 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	537
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	538 $features{ENTRY_ENTRY_ID} = $entry[1] ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	539 $features{ENTRY_ENTRY_NAME} = $entry[2] ;
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	540 $features{ENTRY_FORMULA} = $entry[4] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	541 $features{ENTRY_CPD_MZ} = $entry[5] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	542 $features{ENTRY_ADDUCT} = $entry[6] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	543 $features{ENTRY_ADDUCT_TYPE} = $entry[7] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	544 $features{ENTRY_ADDUCT_MZ} = $entry[8] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	545 $features{ENTRY_DELTA} = $entry[9] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	546
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	547 my %temp = %features ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	548 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	549 }
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	550 # elsif ($line =~ /(\d+\.\d+)/) { #
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	551 # ## 288.082286511284,HMDB0002255,R-Methylmalonyl-CoA, C01213 ,C25H40N7O19P3S,867.131252359,M-3H,-,288.036475,159
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	552 # ## 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
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	553 # ## 174.034120330029,HMDB0011723,2-Methylhippuric acid, C01586,C10H11NO3,193.073893223,M-H20-H,-,174.055503,123
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	554 # ## 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
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	555 # ## 214.018826827064,HMDB0011723,2-Methylhippuric acid, C01586,C10H11NO3,193.073893223,M+Na-2H,-,214.048559,139
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	556 # }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	557 # else {
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	558 #
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	559 # warn "The parsed line ($line) does not match your pattern\n " ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	560 # }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	561 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	562 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	563 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	564 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	565 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	566
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	567 ## manage per query_mzs (keep query masses order by array)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	568 my @results = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	569 foreach (@{$masses}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	570 if ($result_by_entry{$_}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	571
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	572 ## cut all entries > $max_query - all entries were already sorted...by hmdb
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	573 my @temp_entries = @{$result_by_entry{$_}} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	574 my @temp_cut = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	575 my $current_query = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	576 foreach (@temp_entries) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	577 $current_query ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	578 if ($current_query > $max_query) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	579 last ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	580 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	581 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	582 push (@temp_cut, $_) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	583 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	584 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	585 push (@results, \@temp_cut) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	586 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	587 else { push (@results, [] ) ; } ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	588
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	589 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	590 return(\@results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	591 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	592 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	593
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	594 =head2 METHOD parse_hmdb_page_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	595
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	596 ## Description : [DEPRECATED] old HMDB html page parser
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	597 ## Input : $page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	598 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	599 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	600
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	601 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	602 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	603 sub parse_hmdb_page_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	604 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	605 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	606 my ( $page ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	607
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	608 my @results = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	609 my ($catch_table, $catch_name) = (0, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	610 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	611
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	612 if ( defined $page ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	613
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	614 my @page = @{$page} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	615 my $ID = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	616 my @result_by_mz = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	617 my %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	618
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	619 foreach my $line (@page) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	620
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	621 #Section de la page contenant les resultat
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	622 if( $line =~/<table>/ ) { $catch_table = 1 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	623
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	624 ## Si il existe un resultat :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	625 if($catch_table == 1) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	626
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	627 #Id de la molecule, et creation du lien
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	628 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	629 $ID = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	630 $catch_name = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	631 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	632 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	633 #Nom de la molecule ONLY!!
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	634 if ( $catch_name == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	635
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	636 if( $line =~ /<td>(.+)<\/td>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	637
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	638 if ( !defined $name ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	639 $name = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	640 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	641 $result_by_entry{'ENTRY_NAME'} = $name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	642 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	643 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	644 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	645 if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	646 if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	647 if ( !defined $delta ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	648 $delta = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	649 $result_by_entry{'ENTRY_DELTA'} = $delta ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	650 $catch_name = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	651 my %tmp = %result_by_entry ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	652 push (@result_by_mz, \%tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	653 %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	654 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	655 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	656 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	657 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	658 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	659 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	660 #Fin de la section contenant les resultats
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	661 if( $line =~ /<\/table>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	662 $catch_table = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	663 my @Tmp = @result_by_mz ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	664 push(@results, \@Tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	665 @result_by_mz = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	666 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	667 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	668 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	669 return(\@results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	670 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	671 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	672
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	673
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	674 =head2 METHOD get_unik_ids_from_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	675
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	676 ## Description : get all unik ids from the hmdb result object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	677 ## Input : $results
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	678 ## Output : $ids, $idsNumber
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	679 ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	680
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	681 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	682 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	683 sub get_unik_ids_from_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	684 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	685 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	686 my ( $results ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	687 my ( %ids ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	688
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	689 foreach my $result (@{$results}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	690
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	691 foreach my $entries (@{$result}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	692
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	693 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	694 $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	695 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	696 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	697 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	698 my $idsNumber = keys %ids ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	699 return (\%ids, $idsNumber) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	700 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	701 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	702
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	703
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	704
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	705 =head2 METHOD get_hmdb_metabocard_from_id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	706
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	707 ## Description : get a metabocard (xml format from an ID on HMDB)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	708 ## Input : $ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	709 ## Output : $metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	710 ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	711
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	712 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	713 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	714 sub get_hmdb_metabocard_from_id {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	715 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	716 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	717 my ( $ids, $hmdb_url ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	718 my ( %metabocard_features ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	719 my $query = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	720
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	721 ## structure %metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	722 # metabolite_id = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	723 # 'metabolite_name' => '__name__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	724 # 'metabolite_inchi' => '__inchi__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	725 # 'metabolite_logp' => '__logp-ALOGPS__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	726 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	727 # )
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	728
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	729
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	730 if( (defined $ids) and ($ids > 0 ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	731
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	732 foreach my $id (keys %{$ids}) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	733 print "$id...\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	734 my $twig = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	735
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	736 if (defined $hmdb_url) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	737 $query = $hmdb_url.$id.'.xml' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	738
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	739 ## test the header if exists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	740 my $response = head($query) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	741
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	742 if (!defined $response) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	743 $metabocard_features{$id}{'STATUS'} = 'NOT_EXISTING' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	744 $metabocard_features{$id}{'metabolite_name'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	745 $metabocard_features{$id}{'metabolite_inchi'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	746 $metabocard_features{$id}{'metabolite_logp'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	747 ## Need to be improve to manage http 404 or other response diff than 200
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	748 } ## IF error
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	749 elsif ( $response->is_success ) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	750
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	751 $twig = XML::Twig->nparse_ppe(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	752
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	753 twig_handlers => {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	754 # metabolite name
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	755 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; $metabocard_features{$id}{'STATUS'} = 'EXISTING' ; } ,
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	756 # metabolite inchi
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	757 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; $metabocard_features{$id}{'STATUS'} = 'EXISTING' ;} ,
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	758 ## metabolite logP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	759 'metabolite/predicted_properties/property' => sub {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	760
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	761 my ($kind, $source, $value ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	762
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	763 if (defined $_->children ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	764 foreach my $field ($_->children) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	765 if ( $field->name eq 'kind') { $kind = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	766 elsif ( $field->name eq 'source') { $source = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	767 elsif ( $field->name eq 'value') { $value = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	768
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	769 if (defined $source ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	770 if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	771 $metabocard_features{$id}{'metabolite_logp'} = $value ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	772 $metabocard_features{$id}{'STATUS'} = 'EXISTING' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	773 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	774 ($kind, $source, $value ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	775 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	776 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	777 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	778 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	779 },
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	780 pretty_print => 'indented',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	781 error_context => 1, $query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	782 );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	783
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	784 # $twig->print;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	785 $twig->purge ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	786
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	787 # if (!$@) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	788 #
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	789 # }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	790 # else {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	791 # warn $@ ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	792 # }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	793 } ## ELSIF success
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	794 } # END if defined URL
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	795 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	796 warn "\tThe hmdb metabocard url is not defined\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	797 last;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	798 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	799 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	800 } ## End IF defined ids
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	801 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	802 warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	803 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	804
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	805 # print Dumper %metabocard_features ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	806 return (\%metabocard_features) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	807 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	808 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	809
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	810
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	811 =head2 METHOD map_suppl_data_on_hmdb_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	812
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	813 ## Description : map supplementary data with already collected results with hmdb search - delete the entry if hmdb card doesn't exist...
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	814 ## Input : $results, $features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	815 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	816 ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	817
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	818 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	819 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	820 sub map_suppl_data_on_hmdb_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	821 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	822 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	823 my ( $results, $features ) = @_;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	824 my ( @moreResults ) = ( () ) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	825
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	826 foreach my $result (@{$results}) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	827
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	828 my @newResult = () ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	829
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	830 foreach my $entry (@{$result}) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	831
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	832 if ( ($entry->{'ENTRY_ENTRY_ID'}) and ($entry->{'ENTRY_ENTRY_ID'} ne '' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	833
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	834 my $current_id = $entry->{'ENTRY_ENTRY_ID'} ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	835 my $newCompletedEntry = $entry ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	836
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	837 ## If the id exists in feature hash and its status is not NOT_EXISTING
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	838 if ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'EXISTING' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	839
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	840 ## Metabolite NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	841 if (defined $features->{"$current_id"}{'metabolite_name'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	842 $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	843 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	844 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	845 $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	846 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	847 ## Metabolite INCHI
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	848 if (defined $features->{"$current_id"}{'metabolite_inchi'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	849 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	850 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	851 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	852 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NA' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	853 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	854 ## Metabolite LOGP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	855 if (defined $features->{"$current_id"}{'metabolite_logp'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	856 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	857 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	858 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	859 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NA' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	860 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	861 push (@newResult, $newCompletedEntry) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	862 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	863 elsif ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'NOT_EXISTING' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	864 $newCompletedEntry = undef ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	865 next ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	866
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	867 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	868 ## In cas no features are given
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	869 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	870 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NONEDATA' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	871 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NONEDATA' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	872 push (@newResult, $newCompletedEntry) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	873 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	874 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	875 } ## END FOREACH ENTRIES
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	876
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	877 push (@moreResults, \@newResult) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	878
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	879 } ## END FOREACH RESULT
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	880
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	881 return (\@moreResults) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	882 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	883 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	884
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	885
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	886 =head2 METHOD set_html_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	887
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	888 ## Description : initializes and build the tbody object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	889 ## Input : $nb_pages, $nb_items_per_page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	890 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	891 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	892
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	893 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	894 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	895 sub set_html_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	896 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	897 my ( $nb_pages, $nb_items_per_page ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	898
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	899 my ( @tbody_object ) = ( ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	900
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	901 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	902
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	903 my %pages = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	904 # tbody feature
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	905 PAGE_NB => $i,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	906 MASSES => [], ## end MASSES
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	907 ) ; ## end TBODY N
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	908 push (@tbody_object, \%pages) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	909 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	910 return(\@tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	911 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	912 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	913
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	914 =head2 METHOD add_mz_to_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	915
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	916 ## Description : initializes and build the mz object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	917 ## Input : $tbody_object, $nb_items_per_page, $mz_list
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	918 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	919 ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	920
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	921 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	922 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	923 sub add_mz_to_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	924 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	925 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	926
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	927 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	928
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	929 foreach my $page ( @{$tbody_object} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	930
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	931 my @colors = ('white', 'green') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	932 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	933
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	934 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	935 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	936 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	937 $current_index = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	938 last ; ##
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	939 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	940 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	941 $current_index++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	942 if ( $icolor > 1 ) { $icolor = 0 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	943
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	944 if ( exists $mz_list->[$mz_index] ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	945
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	946 my %mz = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	947 # mass feature
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	948 MASSES_ID_QUERY => $ids_list->[$mz_index],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	949 MASSES_MZ_QUERY => $mz_list->[$mz_index],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	950 MZ_COLOR => $colors[$icolor],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	951 MASSES_NB => $mz_index+1,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	952 ENTRIES => [] ,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	953 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	954 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	955 # Html attr for mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	956 $icolor++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	957 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	958 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	959 $mz_index++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	960 } ## foreach mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	961
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	962 $current_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	963 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	964 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	965 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	966 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	967
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	968 =head2 METHOD add_entries_to_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	969
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	970 ## Description : initializes and build the entries object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	971 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	972 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	973 ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	974
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	975 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	976 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	977 sub add_entries_to_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	978 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	979 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	980 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	981
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	982 my $index_page = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	983 my $index_mz_continous = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	984
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	985 foreach my $page (@{$tbody_object}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	986
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	987 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	988
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	989 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	990
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	991 my $index_entry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	992
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	993 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	994 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	995 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	996
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	997 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	998 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	999 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1000 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1001 if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1002 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1003
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1004 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1005
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1006 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1007
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1008 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1009 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1010 ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1011 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1012 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1013 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1014 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1015 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1016 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1017 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1018 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1019 ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1020 ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1021 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1022
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1023 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1024 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1025 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1026 $index_entry++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1027 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1028 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1029 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1030 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1031 ENTRY_ENTRY_NAME => 'UNKNOWN',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1032 ENTRY_ENTRY_ID => 'NONE',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1033 ENTRY_ENTRY_ID2 => '',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1034 ENTRY_FORMULA => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1035 ENTRY_CPD_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1036 ENTRY_ADDUCT => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1037 ENTRY_ADDUCT_TYPE => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1038 ENTRY_ADDUCT_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1039 ENTRY_DELTA => 0,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1040 ENTRY_ENTRY_INCHI => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1041 ENTRY_ENTRY_LOGP => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1042 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1043 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1044 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1045 $index_mz ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1046 $index_mz_continous ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1047 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1048 $index_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1049 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1050 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1051 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1052 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1053
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1054 =head2 METHOD write_html_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1055
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1056 ## Description : prepare and write the html output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1057 ## Input : $html_file_name, $html_object, $html_template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1058 ## Output : $html_file_name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1059 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1060
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1061 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1062 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1063 sub write_html_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1064 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1065 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1066 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1067
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1068 my $html_file = $$html_file_name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1069
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1070 if ( defined $html_file ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1071 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1072
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1073 if (-e $html_template) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1074 my $ohtml = HTML::Template->new(filename => $html_template);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1075 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1076 $ohtml->param( CONDITIONS => $search_condition ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1077 $ohtml->param( PAGES_NB => $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1078 $ohtml->param( PAGES => $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1079 print HTML $ohtml->output ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1080 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1081 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1082 croak "Can't fill any html output : No template available ($html_template)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1083 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1084
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1085 close (HTML) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1086 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1087 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1088 croak "No output file name available to write HTML file\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1089 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1090 return(\$html_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1091 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1092 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1093
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1094 =head2 METHOD set_lm_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1095
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1096 ## Description : build the hmdb_row under its ref form
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1097 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1098 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1099 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1100
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1101 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1102 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1103 sub set_lm_matrix_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1104 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1105 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1106 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1107
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1108 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1109
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1110 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1111 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1112 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1113 push @hmdb_matrix, \@headers ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1114 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1115
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1116 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1117
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1118 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1119
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1120 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1121 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1122 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1123
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1124 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1125 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1126
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1127 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1128
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1129 foreach my $entry (@{ $entries->[$index_mz] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1130
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1131 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1132 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1133 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1134 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1135
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1136 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1137
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1138 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1139
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1140 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1141 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1142 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1143
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1144 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1145 ## entry1=VAR1::VAR2::VAR3::VAR4\|entry2=VAR1::VAR2::VAR3::VAR4\|...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1146 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1147 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'\|' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1148 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1149
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1150 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1151 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1152 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1153 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1154 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1155 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1156 push (@hmdb_matrix, \@clusters) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1157 $index_mz++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1158 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1159 return(\@hmdb_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1160 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1161 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1162
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1163 =head2 METHOD set_hmdb_matrix_object_with_ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1164
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1165 ## Description : build the hmdb_row under its ref form (IDS only)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1166 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1167 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1168 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1169
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1170 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1171 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1172 sub set_hmdb_matrix_object_with_ids {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1173 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1174 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1175 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1176
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1177 # print Dumper $entries ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1178
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1179 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1180
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1181 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1182 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1183
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1184 ## redefined the header hmdb(delta::name::mz::formula::adduct::id)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1185 $header = 'hmdb(delta::name::mz::formula::adduct::id)' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1186 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1187 push @hmdb_matrix, \@headers ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1188 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1189
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1190 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1191
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1192 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1193
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1194 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1195 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1196 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1197
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1198 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1199 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1200
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1201 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1202
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1203 foreach my $entry (@{ $entries->[$index_mz] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1204
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1205 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1206 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1207 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1208 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1209
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1210 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1211
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1212 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1213 ##
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1214
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1215 my ($hmdb_name, $hmdb_id, $hmdb_formula, $hmdb_cpd_mz, $hmdb_adduct, $hmdb_delta) = (undef, undef, undef, undef, undef, undef) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1216
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1217 if ($entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ) { $hmdb_name = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1218 else { $hmdb_name = 'UNKNOWN' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1219
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1220 if ($entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1221 else { $hmdb_id = 0 ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1222
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1223 if ($entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ) { $hmdb_formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1224 else { $hmdb_formula = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1225
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1226 if ($entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ) { $hmdb_cpd_mz = $entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1227 else { $hmdb_cpd_mz = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1228
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1229 if ($entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ) { $hmdb_adduct = $entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1230 else { $hmdb_adduct = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1231
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1232 if ($entries->[$index_mz][$index_entries]{ENTRY_DELTA} ) { $hmdb_delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1233 else { $hmdb_delta = 0 ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1234
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1235
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1236 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1237 ## entry1= ENTRY_DELTA::ENTRY_ENTRY_NAME::ENTRY_CPD_MZ::ENTRY_FORMULA::ENTRY_ADDUCT::ENTRY_ENTRY_ID \| entry2=VAR1::VAR2::VAR3::VAR4\|...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1238 my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1239
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1240 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1241 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' \| ' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1242 else { $cluster_col .= $entry ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1243
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1244 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1245 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1246 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1247 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1248 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1249 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1250 push (@hmdb_matrix, \@clusters) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1251 $index_mz++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1252 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1253 return(\@hmdb_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1254 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1255 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1256
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1257 =head2 METHOD add_lm_matrix_to_input_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1258
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1259 ## Description : build a full matrix (input + lm column)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1260 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1261 ## Output : $output_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1262 ## Usage : my ( $output_matrix_object ) = add_lm_matrix_to_input_matrix( $input_matrix_object, $lm_matrix_object, $nb_header ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1263
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1264 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1265 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1266 sub add_lm_matrix_to_input_matrix {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1267 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1268 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1269 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1270
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1271 my @output_matrix_object = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1272 my $index_row = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1273 my $line = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1274
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1275 foreach my $row ( @{$input_matrix_object} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1276 my @init_row = @{$row} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1277 $line++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1278
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1279 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1280 push (@output_matrix_object, \@init_row) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1281 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1282 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1283
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1284 if ( $lm_matrix_object->[$index_row] ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1285 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1286
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1287 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1288 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1289
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1290 push (@init_row, $lm_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1291 $index_row++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1292 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1293 push (@output_matrix_object, \@init_row) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1294 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1295 return(\@output_matrix_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1296 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1297 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1298
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1299 =head2 METHOD write_csv_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1300
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1301 ## Description : prepare and write csv output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1302 ## Input : $csv_file, $rows
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1303 ## Output : $csv_file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1304 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1305
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1306 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1307 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1308 sub write_csv_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1309 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1310 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1311 my ( $csv_file, $rows ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1312
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1313 # my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1314 my $ocsv = lib::csv::new() ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1315 my $csv = $ocsv->get_csv_object("\t") ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1316 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1317
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1318 return($csv_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1319 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1320 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1321
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1322 =head2 METHOD write_csv_one_mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1323
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1324 ## Description : print a cvs file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1325 ## Input : $masses, $ids, $results, $file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1326 ## Output : N/A
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1327 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1328
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1329 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1330 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1331 sub write_csv_one_mass {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1332 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1333 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1334 my ( $masses, $ids, $results, $file, ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1335
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1336 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1337 print CSV "ID\tQuery(Da)\tDelta(ppm)\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1338
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1339 my $i = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1340
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1341 foreach my $id (@{$ids}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1342 my $mass = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1343 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1344 else { last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1345
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1346 if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1347
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1348 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1349 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1350 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1351
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1352 foreach my $entry (@{$results->[$i]}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1353 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1354 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1355 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1356 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1357 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1358 # print "\n-----------------------" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1359 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1360 # print "-------------------------$check_rebond\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1361 # print Dumper @anti_redondant ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1362 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1363
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1364 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1365
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1366 print CSV "$id\t$mass\t" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1367
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1368 ## print delta
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1369 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1370 else { print CSV "0\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1371
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1372 ## print cpd name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1373 if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1374 else { print CSV "UNKNOWN\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1375
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1376 ## print cpd mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1377 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1378 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1379
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1380 ## print cpd formula
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1381 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1382 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1383
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1384 ## print adduct
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1385 if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1386 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1387
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1388 ## print adduct mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1389 if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1390 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1391
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1392 ## print cpd id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1393 if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1394 else { print CSV "N/A\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1395 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1396 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1397 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1398 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1399 print CSV "$id\t$mass\t0\tUNKNOWN\tN/A\tN/A\tN/A\tN/A\tN/A\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1400 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1401 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1402 $i++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1403 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1404 close(CSV) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1405 return() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1406 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1407 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1408
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1409 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1410
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1411
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1412 __END__
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1413
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1414 =head1 SUPPORT
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1415
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1416 You can find documentation for this module with the perldoc command.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1417
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1418 perldoc hmdb.pm
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1419
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1420 =head1 Exports
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1421
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1422 =over 4
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1423
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1424 =item :ALL is ...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1425
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1426 =back
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1427
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1428 =head1 AUTHOR
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1429
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1430 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1431
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1432 =head1 LICENSE
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1433
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1434 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	1435
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1436 =head1 VERSION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1437
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1438 version 1 : 06 / 06 / 2013
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1439
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1440 version 2 : 27 / 01 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1441
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1442 version 3 : 19 / 11 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1443
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1444 version 4 : 28 / 01 / 2016
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1445
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1446 version 5 : 02 / 11 /2016
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1447
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1448 =cut

Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate lib/hmdb.pm @ 22:453fbe98925a draft