hmdb_ms_search: lib/hmdb.pm annotate

annotate lib/hmdb.pm @ 29:29195cb5d378 draft default tip

master branch Updating with tag :CI_COMMIT_TAG - - Fxx

author	fgiacomoni
date	Tue, 04 Jun 2024 09:42:17 +0000
parents	76872ac24fb2
children

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 ;
26 76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	17 use URI::Encode ;
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	18 use open qw( :std :encoding(UTF-8) );
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	19
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	20 use Data::Dumper ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	21
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	22 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	23
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	24 our $VERSION = "1.0";
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	25 our @ISA = qw(Exporter);
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	26 our @EXPORT = qw( parseHmdb5CSVResults getMatchesFromHmdb5WithUA map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	27 our %EXPORT_TAGS = ( ALL => [qw( parseHmdb5CSVResults getMatchesFromHmdb5WithUA map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] );
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	28
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	29 =head1 NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	30
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	31 My::Module - An example module
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	32
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	33 =head1 SYNOPSIS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	34
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	35 use My::Module;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	36 my $object = My::Module->new();
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	37 print $object->as_string;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	38
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	39 =head1 DESCRIPTION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	40
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	41 This module does not really exist, it
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	42 was made for the sole purpose of
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	43 demonstrating how POD works.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	44
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	45 =head1 METHODS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	46
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	47 Methods are :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	48
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	49 =head2 METHOD new
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	50
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	51 ## Description : new
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	52 ## Input : $self
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	53 ## Ouput : bless $self ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	54 ## Usage : new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	55
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	56 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	57
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	58 sub new {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	59 ## Variables
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	60 my $self={};
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	61 bless($self) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	62 return $self ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	63 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	64 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	65
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	66
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	67 =head2 METHOD extract_sub_mz_lists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	68
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	69 ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	70 ## Input : $HMDB_LIMITS, $masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	71 ## Output : $sublists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	72 ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	73
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	74 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	75 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	76 sub extract_sub_mz_lists {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	77 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	78 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	79 my ( $masses, $HMDB_LIMITS ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	80
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	81 my ( @sublists, @sublist ) = ( (), () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	82 my $nb_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	83 my $nb_total_mzs = scalar(@{$masses}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	84
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	85 if ($nb_total_mzs == 0) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	86 die "The provided mzs list is empty" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	87 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	88
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	89 for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	90
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	91 if ( $nb_mz < $HMDB_LIMITS ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	92 if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	93 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	94 elsif ( $nb_mz == $HMDB_LIMITS ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	95 my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	96 $current_pos-- ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	97 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	98 if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	99 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	100 return(\@sublists) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	101 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	102 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	103
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	104 =head2 METHOD prepare_multi_masses_query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	105
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	106 ## Description : Generate the adapted format of the mz list for HMDB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	107 ## Input : $masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	108 ## Output : $hmdb_masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	109 ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	110
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	111 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	112 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	113 sub prepare_multi_masses_query {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	114 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	115 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	116 my ( $masses ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	117
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	118 my $hmdb_masses = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	119 my $sep = '%0D%0A' ; ## retour chariot encode
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	120 my ($nb_masses, $i) = (0, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	121
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	122 if ( defined $masses ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	123 my @masses = @{$masses} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	124 my $nb_masses = scalar ( @masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	125 if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; }
6 7ed37640fe2a planemo upload commit 4c72059b94b27eda2c0ee89bfc5f9bf4e3425dc5 fgiacomoni parents: 4 diff changeset	126 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	127
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	128 foreach my $mass (@masses) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	129
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	130 if ($i < $nb_masses) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	131 $hmdb_masses .= $mass.$sep ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	132 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	133 elsif ( $i == $nb_masses ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	134 $hmdb_masses .= $mass ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	135 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	136 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	137 last ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	138 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	139 $i ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	140 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	141 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	142 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	143 croak "No mass list found \n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	144 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	145 return($hmdb_masses, $nb_masses) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	146 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	147 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	148
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	149
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	150 =head2 METHOD prepareAdductListFormat
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	151
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	152 ## Description : prepare a adduct list well formatted for https queries
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	153 ## Input : $adductString
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	154 ## Output : $formattedAdductString
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	155 ## Usage : my ( $formattedAdductString ) = prepareAdductListFormat ( $adductString ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	156
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	157 =cut
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	158 ## START of SUB
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	159 sub prepareAdductListFormat {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	160 ## Retrieve Values
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	161 my $self = shift ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	162 my ( $adductString ) = @_;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	163 my ( $formattedAdductString, $nbAdducts ) = ( undef, 0 ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	164
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	165 ## Formatting is converting [+] in %2B, [-] as - and [,] in converted space as 'M%2BH%202M%2BH' for 'M+H,2M+2H'
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	166 # print "\t$adductString ..." ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	167
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	168 if (defined $adductString) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	169
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	170 ## counting selected adducts
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	171 $nbAdducts = scalar( my @adducts = ( split (/,/, $adductString) ) ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	172
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	173 ## Converting string into http post format
26 76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	174 # $adductString =~ s/\+/%2B/g ;
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	175 # $adductString =~ s/,/%20/g ;
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	176 # $formattedAdductString = $adductString ;
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	177
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	178 my $uri = URI::Encode->new( { encode_reserved => 1 } );
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	179 foreach my $adduct (@adducts) {
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	180 # &results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	181 my $EncodedAdduct = $uri->encode($adduct);
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	182 $formattedAdductString .= '&results%5Badduct_type%5D%5B%5D='.$EncodedAdduct ;
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	183 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	184 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	185 else {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	186 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	187 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	188
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	189 # print "->$formattedAdductString\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	190
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	191 return ($formattedAdductString, $nbAdducts) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	192 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	193 ### END of SUB
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	194
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	195 =head2 METHOD test_matches_from_hmdb_ua DEPRECATED
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	196
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	197 ## 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	198 ## Input : none
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	199 ## Output : $status_line
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	200 ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	201
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	202 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	203 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	204 sub test_matches_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	205 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	206 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	207
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	208 my @page = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	209
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	210 my $ua = new LWP::UserAgent;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	211 $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	212
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	213 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	214 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	215
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	216 my $req = HTTP::Request->new('POST', $url, $header);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	217 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	218
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	219 ## Query format for HMDB 4.0
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	220 #"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	221
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	222 $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	223 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	224 my $res = $ua->request($req);
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	225
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	226 print $res->as_string;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	227 my $status_line = $res->status_line ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	228 ($status_line) = ($status_line =~ /(\d+)/);
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	229
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	230 return (\$status_line) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	231 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	232 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	233
22 453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	234
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	235 =head2 METHOD checkHmdbUrlEntries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	236
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	237 ## 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	238 ## Input : $urlRoot, $entries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	239 ## Output : $validEntries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	240 ## Usage : my ( $validEntries ) = checkHmdbUrlEntries ( $entries ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	241
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	242 =cut
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	243 ## START of SUB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	244 sub checkHmdbUrlEntries {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	245 ## Retrieve Values
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	246 my $self = shift ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	247 my ( $urlRoot, $clusters, $maxQuery ) = @_;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	248 my ( @ValidResults, @validFeature ) = ( (), () ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	249
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	250 foreach my $resultsByMass (@{$clusters}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	251 my $currentQuery = 0 ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	252 foreach my $feature (@{$resultsByMass}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	253
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	254 if ($feature->{ENTRY_ENTRY_ID}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	255
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	256 my $url = $urlRoot.$feature->{ENTRY_ENTRY_ID} ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	257 if ( get($url)) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	258 $currentQuery ++ ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	259 if ($currentQuery > $maxQuery) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	260 last ;
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 else {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	263 push (@validFeature, $feature) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	264 # print "Url is valid ($url) - - add to final results\n" ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	265 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	266 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	267 else {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	268 # 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	269 next ;
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 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	272 } # END FOREACH FEATURE
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	273 my @tmp = @validFeature ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	274 push (@ValidResults, \@tmp) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	275 @validFeature = () ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	276 } # END FOREACH RESULTS
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	277
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	278 return (\@ValidResults) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	279 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	280 ### END of SUB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	281
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	282
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	283 =head2 METHOD testMatchesFromHmdbWithUA
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	284
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	285 ## Description : [DEPRECATED] test a single query with tests parameters on hmdb - get the status of the complete server infra.
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	286 ## Input : none
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	287 ## Output : $status_line
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	288 ## Usage : my ( $status_line ) = testMatchesFromHmdbWithUA( ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	289
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	290 =cut
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	291 ## START of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	292 sub testMatchesFromHmdbWithUA {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	293 ## Retrieve Values
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	294 my $self = shift ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	295
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	296 my @page = () ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	297 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	298
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	299 my $mech = WWW::Mechanize->new(
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	300 # agent => 'wonderbot for W4M 1.01',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	301 agent => 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.14; rv:93.0) Gecko/20100101 Firefox/93.0' ,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	302 autocheck => 0,
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	303 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	304
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	305 my $statusGetLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	306 my $statusPostLine = 0 ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	307 my $csrftoken = undef ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	308
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	309 #receiving cookies and authentication token (CFRS)
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	310 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	311 $statusGetLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	312
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	313 if ($statusGetLine == 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	314 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	315 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	316 $csrftoken = $1;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	317 print "\nTOKEN: $csrftoken\n" ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	318 $mech->add_header("X-CSRFToken", $csrftoken);
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	319 $mech->add_header('Host', 'specdb.wishartlab.com');
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	320 $mech->add_header('Connection', 'keep-alive');
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	321 $mech->add_header('Upgrade-Insecure-Requests', '1');
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	322 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	323 $mech->add_header('Accept-Language', 'en-US,en;q=0.5');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	324 $mech->add_header('Accept-Encoding', 'gzip, deflate');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	325 # $mech->add_header('Content-Length', "300");
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	326 $mech->add_header('Origin', 'null');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	327 $mech->add_header('DNT', '1');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	328 $mech->add_header('Referer', 'https://hmdb.ca/spectra/ms/search');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	329 # $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	330 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,/;q=0.8');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	331
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	332
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	333 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	334
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	335 ## POST test
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	336 my $top = 1 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	337 while ($statusPostLine != 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	338
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	339 # Fix a limit at 3 tries...
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	340 if ($top < 4) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	341 print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	342 eval {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	343 $mech->post(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	344 "http://specdb.wishartlab.com/ms/search.csv",
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	345 Content => 'utf8=TRUE&authenticity_token='.$csrftoken.'&mode=positive&adduct_type=M%2BH%202M%2BH&query_masses=125.0089&tolerance=0.001&database=HMDB&commit=Download Results As CSV'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	346 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	347 } ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	348 # print Dumper $mech ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	349 $statusPostLine = $mech->status() ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	350 print "Status: $statusPostLine" ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	351 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	352 else {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	353 last ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	354 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	355 $top++ ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	356 }## End While
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	357 return (\$statusPostLine) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	358 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	359 ## END of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	360
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	361
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	362 =head2 METHOD testMatchesFromHmdb5WithUA
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	363
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	364 ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra (API V5.0 compliant).
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	365 ## Input : none
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	366 ## Output : $status_line
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	367 ## Usage : my ( $status_line ) = testMatchesFromHmdb5WithUA( ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	368
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	369 =cut
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	370 ## START of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	371 sub testMatchesFromHmdb5WithUA {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	372 ## Retrieve Values
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	373 my $self = shift ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	374
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	375 my $mech = WWW::Mechanize->new(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	376 agent => 'wonderbot for W4M 3.0',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	377 autocheck => 1,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	378 timeout => 2400,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	379 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	380
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	381 my $statusGetLine = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	382 my $statusPostLine = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	383
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	384 #receiving cookies and authentication token (CFRS)
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	385 my $reqInit = $mech->get("https://www.hmdb.ca/spectra/ms/search");
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	386 $statusGetLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	387
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	388 if ($statusGetLine == 200 ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	389 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	390 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	391 my $csrftoken = $1;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	392 # print "\nTOKEN: $csrftoken\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	393 $mech->add_header("X-CSRFToken", $csrftoken);
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	394 $mech->add_header('Connection', 'keep-alive');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	395 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	396 $mech->add_header('Referer', 'https://www.hmdb.ca/spectra/ms/search');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	397 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	398 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	399
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	400
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	401 ## POST test
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	402 my $top = 1 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	403 while ($statusPostLine != 200 ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	404
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	405 # Fix a limit at 3 tries...
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	406 if ($top < 4) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	407 print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	408 eval {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	409 my $res = $mech->get(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	410 'https://hmdb.ca/spectra/ms/generate_csv.csv?'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	411 .'results%5Baction%5D=search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	412 .'&results%5Badduct_type%5D%5B%5D=M%2BH%202M%2BH'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	413 #.'&results%5Bauthenticity_token%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	414 .'&results%5Bccs_predictors%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	415 .'&results%5Bccs_tolerance%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	416 .'&results%5Bcommit%5D=Search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	417 .'&results%5Bcontroller%5D=specdb%2Fms'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	418 .'&results%5Bms_search_ion_mode%5D=positive'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	419 .'&results%5Bquery_masses%5D=125.0089'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	420 .'&results%5Btolerance%5D=0.001'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	421 .'&results%5Btolerance_units%5D=Da'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	422 .'&results%5Butf8%5D=%E2%9C%93'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	423
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	424 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	425 } ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	426 # print Dumper $mech ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	427 $statusPostLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	428 print "Status: $statusPostLine" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	429 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	430 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	431 last ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	432 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	433 $top++ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	434 }## End While
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	435 return (\$statusPostLine) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	436 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	437 ## END of SUB
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	438
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	439 =head2 METHOD check_state_from_hmdb_ua
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	440
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	441 ## Description : check the thhp status of hmdb and kill correctly the script if necessary.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	442 ## Input : $status
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	443 ## Output : none
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	444 ## Usage : check_state_from_hmdb_ua($status) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	445
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	446 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	447 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	448 sub check_state_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	449 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	450 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	451 my ($status) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	452
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	453 if (!defined $$status) {
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	454 croak "No https status is defined for the distant server" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	455 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	456 else {
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	457 unless ( $$status == 200 ) {
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	458 if ( $$status == 502 ) { croak "Bad Gateway (502): The HMDB server, while acting as a gateway or proxy, received an invalid response from the upstream server. The Hmdb tool is stopped with error." ; }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	459 if ( $$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	460 if ( $$status == 500 ) { croak "Internal Server Error (500): The HMDB server returns an unexpected internal server error. The Hmdb tool is stopped with error." ; }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	461 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	462 ## None supported http code error ##
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	463 croak "Internal Server Error $$status..." ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	464 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	465 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	466 if ( $$status == 200 ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	467 print "\tThe HMDB server returns that your request (connexion test) was fulfilled\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	468 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	469 }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	470 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	471
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	472 return (1) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	473 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	474 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	475
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	476 =head2 METHOD get_matches_from_hmdb_ua DEPRECATED
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	477
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	478 ## 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	479 ## Input : $mass, $delta, $mode
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	480 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	481 ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	482
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	483 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	484 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	485 sub get_matches_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	486 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	487 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	488 my ( $masses, $delta, $mode ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	489
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	490 ## Added May, 2022
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	491 warn "[DEPRECATED Methode] method get_matches_from_hmdb_ua is deprecated and not compatible with HMDB 4.0" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	492 return ([], 500) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	493
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	494 my @page = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	495
8 97788e4bf3fc planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392-dirty fgiacomoni parents: 6 diff changeset	496 my $ua = LWP::UserAgent->new( keep_alive => 10 );
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	497 $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	498 $ua->timeout(2400) ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	499
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	500 # Cookies
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	501 # my $cookie = new HTTP::Cookies( ignore_discard => 1 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	502 # $ua->cookie_jar( $cookie );
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	503
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	504 # my $req = HTTP::Request->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	505 # POST => 'http://specdb.wishartlab.com/ms/search.csv');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	506
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	507 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	508 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	509 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	510 my $encoded_data = encode_utf8($data);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	511
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	512 my $req = HTTP::Request->new('POST', $url, $header, $encoded_data);
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	513
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	514 # $req->content_type('application/x-www-form-urlencoded');
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	515 $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	516 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	517 my $res = $ua->request($req);
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	518 my $status_line = undef ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	519 print $res->as_string;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	520 if ($res->is_success) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	521 @page = split ( /\n/, $res->decoded_content ) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	522 $status_line = 'OK' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	523 } else {
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	524 $status_line = $res->status_line ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	525 ($status_line) = ($status_line =~ /(\d+)/);
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 15 diff changeset	526 warn "\t[HMDB service issue !! the server returned a $status_line HTTP error]" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	527 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	528
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	529
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	530 return (\@page, $status_line) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	531 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	532 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	533
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	534 =head2 METHOD getMatchesFromHmdbWithUA
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	535
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	536 ## 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	537 ## Input : $mass, $delta, $mode, adducts
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	538 ## Output : $results
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	539 ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	540
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	541 =cut
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	542 ## START of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	543 sub getMatchesFromHmdbWithUA {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	544 ## Retrieve Values
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	545 my $self = shift ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	546 my ( $masses, $delta, $mode, $adducts ) = @_ ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	547
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	548 ## Added May, 2022
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	549 warn "[DEPRECATED Methode] method getMatchesFromHmdbWithUA is deprecated and not compatible with HMDB 5.0" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	550 return ([], 500) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	551
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	552 my @page = () ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	553
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	554 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	555
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	556 my $mech = WWW::Mechanize->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	557 agent => 'wonderbot for W4M 1.01',
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	558 autocheck => 1,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	559 timeout => 2400,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	560 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	561
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	562 my $statusGetLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	563 my $statusPostLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	564
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	565 #receiving cookies and authentication token (CFRS)
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	566 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	567 $statusGetLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	568
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	569 if ($statusGetLine == 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	570 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	571 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	572 my $csrftoken = $1;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	573 # print "\nTOKEN: $csrftoken\n" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	574 $mech->add_header("X-CSRFToken", $csrftoken);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	575 $mech->add_header('Connection', 'keep-alive');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	576 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	577 $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	578 $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	579 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	580 ## adduct format is adduct_type=M%2BH%202M%2BH
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	581
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	582 if ( (!defined $adducts) or ( $adducts eq '') ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	583 $adducts = 'Unknown' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	584 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	585
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	586 my $res = $mech->post(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	587 "http://specdb.wishartlab.com/ms/search.csv",
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	588 Content => 'utf8=TRUE&mode='
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	589 .$mode.'&adduct_type='
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	590 .$adducts.'&query_masses='
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	591 .$masses.'&tolerance='
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	592 .$delta.'&database=HMDB&commit=Download Results As CSV'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	593 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	594
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	595 if ($mech->success) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	596 @page = split ( /\n/, $res->decoded_content ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	597 $statusPostLine = 'OK' ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	598 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	599 else {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	600 $statusPostLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	601 warn "\t[HMDB service issue !! the server returned a $statusPostLine HTTP error]" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	602 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	603
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	604 # print Dumper $res->decoded_content ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	605
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	606 return (\@page, $statusPostLine) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	607 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	608 ## END of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	609
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	610 =head2 METHOD getMatchesFromHmdb5WithUA
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	611
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	612 ## Description : HMDB v5.0 querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	613 ## Input : $mass, $delta, $mode, adducts
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	614 ## Output : $results
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	615 ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	616
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	617 =cut
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	618 ## START of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	619 sub getMatchesFromHmdb5WithUA {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	620 ## Retrieve Values
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	621 my $self = shift ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	622 my ( $masses, $delta, $mode, $adducts ) = @_ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	623
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	624 my @page = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	625
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	626 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	627
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	628 my $mech = WWW::Mechanize->new(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	629 agent => 'wonderbot for W4M 3.0',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	630 autocheck => 1,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	631 timeout => 2400,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	632 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	633
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	634 my $statusGetLine = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	635 my $statusPostLine = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	636
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	637 #receiving cookies and authentication token (CFRS)
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	638 my $reqInit = $mech->get("https://www.hmdb.ca/spectra/ms/search");
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	639 $statusGetLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	640
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	641 if ($statusGetLine == 200 ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	642 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	643 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	644 my $csrftoken = $1;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	645 # print "\nTOKEN: $csrftoken\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	646 $mech->add_header("X-CSRFToken", $csrftoken);
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	647 $mech->add_header('Connection', 'keep-alive');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	648 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	649 $mech->add_header('Referer', 'https://www.hmdb.ca/spectra/ms/search');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	650 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	651 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	652 if ( (!defined $adducts) or ( $adducts eq '') ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	653 $adducts = 'Unknown' ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	654 }
26 76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	655 #&results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	656 # Query
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	657 #https://hmdb.ca/spectra/ms/generate_csv.csv?results%5Baction%5D=search&results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa&results%5Bauthenticity_token%5D=uN4r4Xme0bl5Lj%2Buv%2BrjebgrdF0oFO7mfxg0T7mHFlHcUSDkVAd%2BRB3qQDzm5fdz3BV4kKX%2F1i2uLOOdvBgK%2FA%3D%3D&results%5Bccs_predictors%5D=&results%5Bccs_tolerance%5D=&results%5Bcommit%5D=Search&results%5Bcontroller%5D=specdb%2Fms&results%5Bms_search_ion_mode%5D=positive&results%5Bquery_masses%5D=175.01&results%5Btolerance%5D=0.05&results%5Btolerance_units%5D=Da&results%5Butf8%5D=%E2%9C%93
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	658 #&results%5Badduct_type%5D%5B%5D=M%2BH&results%5Badduct_type%5D%5B%5D=M%2BNH4-H2O&results%5Badduct_type%5D%5B%5D=M%2BNa
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	659
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	660 my $res = $mech->get(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	661 'https://hmdb.ca/spectra/ms/generate_csv.csv?'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	662 .'results%5Baction%5D=search'
26 76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	663 #.'&results%5Badduct_type%5D%5B%5D='.$adducts
76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	664 .$adducts
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	665 #.'&results%5Bauthenticity_token%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	666 .'&results%5Bccs_predictors%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	667 .'&results%5Bccs_tolerance%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	668 .'&results%5Bcommit%5D=Search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	669 .'&results%5Bcontroller%5D=specdb%2Fms'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	670 .'&results%5Bms_search_ion_mode%5D='.$mode
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	671 .'&results%5Bquery_masses%5D='.$masses
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	672 .'&results%5Btolerance%5D='.$delta
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	673 .'&results%5Btolerance_units%5D=Da'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	674 .'&results%5Butf8%5D=%E2%9C%93'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	675
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	676 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	677 $statusGetLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	678
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	679 if ($mech->success) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	680 @page = split ( /\n/, $res->decoded_content ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	681 $statusPostLine = 'OK' ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	682 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	683 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	684 $statusPostLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	685 warn "\t[HMDB service issue !! the server returned a $statusPostLine HTTP error]" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	686 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	687
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	688 # print Dumper $res->decoded_content ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	689
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	690 return (\@page, $statusPostLine) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	691 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	692 ## END of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	693
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	694
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	695 =head2 METHOD parseHmdb5CSVResults
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	696
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	697 ## Description : parse the csv results and get data - API 5.0 compliant
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	698 ## Input : $csv
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	699 ## Output : $results
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	700 ## Usage : my ( $results ) = parseHmdb5CSVResults( $csv ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	701
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	702 =cut
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	703 ## START of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	704 sub parseHmdb5CSVResults {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	705 ## Retrieve Values
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	706 my $self = shift ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	707 my ( $csv, $masses, $max_query ) = @_ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	708
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	709 my $test = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	710 my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	711
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	712 my %result_by_entry = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	713 my %features = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	714
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	715 # print Dumper $csv ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	716 # print Dumper $masses ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	717 # print Dumper $max_query ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	718
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	719 foreach my $line (@{$csv}) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	720 ## NEW HMDB format V5.0 - May2022
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	721 if ($line !~ /query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,"delta$ppm$,",ccs_value/) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	722 #query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	723
25 8f7546d0b925 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 24 diff changeset	724 #if ( $line =~ /(\d+\.\d+),(\w+),(.),(\w+),(\d+\.\d+),([\+\|\-\|\w\|n\/a\|\s+]+)\s,(\+\|\-),(\d+\.\d+),(\d+),(\d*)/ ) {
8f7546d0b925 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 24 diff changeset	725 if ( $line =~ /(\d+\.\d+),(\w+),(.),(\w+),(\d+\.\d+),([\+\|\-\|\w\|n\/a\|\s+]+)\s,(\+\|\-),(\d+\.\d+),(\d+),.*/ ) { # works on NEG AND POS results
8f7546d0b925 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 24 diff changeset	726 print "$line\n" ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	727 #if ( $line =~ /(\d+\.\d+),(\w+),(.),([\w\|n\/a\|\s+]+)\s,(\w+),(\d+\.\d+),(.*),(\+\|\-),(\d+\.\d+),(\d+)/ ) {
25 8f7546d0b925 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 24 diff changeset	728 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9") ;
8f7546d0b925 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 24 diff changeset	729 #my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	730
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	731 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	732
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	733 $features{ENTRY_ENTRY_ID} = $entry[1] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	734 $features{ENTRY_ENTRY_NAME} = $entry[2] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	735 $features{ENTRY_FORMULA} = $entry[3] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	736 $features{ENTRY_CPD_MZ} = $entry[4] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	737 $features{ENTRY_ADDUCT} = $entry[5] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	738 $features{ENTRY_ADDUCT_TYPE} = $entry[6] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	739 $features{ENTRY_ADDUCT_MZ} = $entry[7] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	740 $features{ENTRY_DELTA} = $entry[8] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	741
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	742 my %temp = %features ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	743 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	744 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	745 # elsif ($line =~ /(\d+\.\d+)/) { #
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	746 # ## 288.082286511284,HMDB0002255,R-Methylmalonyl-CoA, C01213 ,C25H40N7O19P3S,867.131252359,M-3H,-,288.036475,159
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	747 # ## 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
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	748 # ## 174.034120330029,HMDB0011723,2-Methylhippuric acid, C01586,C10H11NO3,193.073893223,M-H20-H,-,174.055503,123
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	749 # ## 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
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	750 # ## 214.018826827064,HMDB0011723,2-Methylhippuric acid, C01586,C10H11NO3,193.073893223,M+Na-2H,-,214.048559,139
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	751 # }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	752 # else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	753 #
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	754 # warn "The parsed line ($line) does not match your pattern\n " ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	755 # }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	756 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	757 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	758 print "Header detected...Parsing is starting...\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	759 next ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	760 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	761 } ## end foreach
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	762
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	763 ## manage per query_mzs (keep query masses order by array)
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	764 my @results = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	765 foreach (@{$masses}) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	766 if ($result_by_entry{$_}) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	767
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	768 ## cut all entries > $max_query - all entries were already sorted...by hmdb
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	769 my @temp_entries = @{$result_by_entry{$_}} ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	770 my @temp_cut = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	771 my $current_query = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	772 foreach (@temp_entries) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	773 $current_query ++ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	774 if ($current_query > $max_query) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	775 last ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	776 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	777 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	778 push (@temp_cut, $_) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	779 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	780 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	781 push (@results, \@temp_cut) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	782 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	783 else { push (@results, [] ) ; } ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	784
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	785 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	786 return(\@results) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	787 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	788 ## END of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	789
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	790
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	791 =head2 METHOD parse_hmdb_csv_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	792
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	793 ## Description : [DEPRECATED] parse the csv results and get data
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	794 ## Input : $csv
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	795 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	796 ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	797
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	798 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	799 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	800 sub parse_hmdb_csv_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	801 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	802 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	803 my ( $csv, $masses, $max_query ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	804
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	805 my $test = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	806 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	807
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	808 my %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	809 my %features = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	810
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	811 # print Dumper $csv ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	812 # print Dumper $masses ;
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	813 # print Dumper $max_query ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	814
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	815 foreach my $line (@{$csv}) {
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	816 ## NEW HMDB format V4.0 - dec2017
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	817 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	818
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	819 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	820 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	821
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	822 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	823
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	824 $features{ENTRY_ENTRY_ID} = $entry[1] ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	825 $features{ENTRY_ENTRY_NAME} = $entry[2] ;
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	826 $features{ENTRY_FORMULA} = $entry[4] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	827 $features{ENTRY_CPD_MZ} = $entry[5] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	828 $features{ENTRY_ADDUCT} = $entry[6] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	829 $features{ENTRY_ADDUCT_TYPE} = $entry[7] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	830 $features{ENTRY_ADDUCT_MZ} = $entry[8] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	831 $features{ENTRY_DELTA} = $entry[9] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	832
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	833 my %temp = %features ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	834 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	835 }
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	836 # elsif ($line =~ /(\d+\.\d+)/) { #
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	837 # ## 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	838 # ## 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	839 # ## 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	840 # ## 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	841 # ## 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	842 # }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	843 # else {
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	844 #
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	845 # warn "The parsed line ($line) does not match your pattern\n " ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	846 # }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	847 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	848 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	849 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	850 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	851 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	852
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	853 ## manage per query_mzs (keep query masses order by array)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	854 my @results = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	855 foreach (@{$masses}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	856 if ($result_by_entry{$_}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	857
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	858 ## cut all entries > $max_query - all entries were already sorted...by hmdb
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	859 my @temp_entries = @{$result_by_entry{$_}} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	860 my @temp_cut = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	861 my $current_query = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	862 foreach (@temp_entries) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	863 $current_query ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	864 if ($current_query > $max_query) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	865 last ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	866 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	867 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	868 push (@temp_cut, $_) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	869 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	870 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	871 push (@results, \@temp_cut) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	872 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	873 else { push (@results, [] ) ; } ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	874
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	875 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	876 return(\@results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	877 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	878 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	879
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	880 =head2 METHOD parse_hmdb_page_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	881
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	882 ## Description : [DEPRECATED] old HMDB html page parser
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	883 ## Input : $page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	884 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	885 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	886
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	887 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	888 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	889 sub parse_hmdb_page_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	890 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	891 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	892 my ( $page ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	893
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	894 my @results = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	895 my ($catch_table, $catch_name) = (0, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	896 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	897
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	898 if ( defined $page ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	899
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	900 my @page = @{$page} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	901 my $ID = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	902 my @result_by_mz = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	903 my %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	904
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	905 foreach my $line (@page) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	906
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	907 #Section de la page contenant les resultat
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	908 if( $line =~/<table>/ ) { $catch_table = 1 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	909
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	910 ## Si il existe un resultat :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	911 if($catch_table == 1) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	912
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	913 #Id de la molecule, et creation du lien
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	914 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	915 $ID = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	916 $catch_name = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	917 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	918 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	919 #Nom de la molecule ONLY!!
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	920 if ( $catch_name == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	921
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	922 if( $line =~ /<td>(.+)<\/td>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	923
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	924 if ( !defined $name ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	925 $name = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	926 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	927 $result_by_entry{'ENTRY_NAME'} = $name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	928 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	929 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	930 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	931 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	932 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	933 if ( !defined $delta ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	934 $delta = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	935 $result_by_entry{'ENTRY_DELTA'} = $delta ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	936 $catch_name = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	937 my %tmp = %result_by_entry ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	938 push (@result_by_mz, \%tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	939 %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	940 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	941 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	942 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	943 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	944 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	945 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	946 #Fin de la section contenant les resultats
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	947 if( $line =~ /<\/table>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	948 $catch_table = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	949 my @Tmp = @result_by_mz ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	950 push(@results, \@Tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	951 @result_by_mz = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	952 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	953 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	954 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	955 return(\@results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	956 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	957 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	958
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	959
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	960 =head2 METHOD get_unik_ids_from_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	961
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	962 ## Description : get all unik ids from the hmdb result object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	963 ## Input : $results
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	964 ## Output : $ids, $idsNumber
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	965 ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	966
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	967 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	968 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	969 sub get_unik_ids_from_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	970 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	971 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	972 my ( $results ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	973 my ( %ids ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	974
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	975 foreach my $result (@{$results}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	976
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	977 foreach my $entries (@{$result}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	978
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	979 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	980 $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	981 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	982 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	983 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	984 my $idsNumber = keys %ids ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	985 return (\%ids, $idsNumber) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	986 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	987 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	988
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	989
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	990
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	991 =head2 METHOD get_hmdb_metabocard_from_id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	992
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	993 ## Description : get a metabocard (xml format from an ID on HMDB)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	994 ## Input : $ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	995 ## Output : $metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	996 ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	997
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	998 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	999 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1000 sub get_hmdb_metabocard_from_id {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1001 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1002 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1003 my ( $ids, $hmdb_url ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1004 my ( %metabocard_features ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1005 my $query = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1006
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1007 ## structure %metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1008 # metabolite_id = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1009 # 'metabolite_name' => '__name__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1010 # 'metabolite_inchi' => '__inchi__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1011 # 'metabolite_logp' => '__logp-ALOGPS__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1012 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1013 # )
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1015
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1016 if( (defined $ids) and ($ids > 0 ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1017
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1018 foreach my $id (keys %{$ids}) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1019 print "$id...\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1020 my $twig = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1021
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1022 if (defined $hmdb_url) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1023 $query = $hmdb_url.$id.'.xml' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1024
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1025 ## test the header if exists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1026 my $response = head($query) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1027
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1028 if (!defined $response) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1029 $metabocard_features{$id}{'STATUS'} = 'NOT_EXISTING' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1030 $metabocard_features{$id}{'metabolite_name'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1031 $metabocard_features{$id}{'metabolite_inchi'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1032 $metabocard_features{$id}{'metabolite_logp'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1033 ## 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	1034 } ## IF error
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1035 elsif ( $response->is_success ) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1036
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1037 $twig = XML::Twig->nparse_ppe(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1038
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1039 twig_handlers => {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1040 # metabolite name
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1041 '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	1042 # metabolite inchi
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1043 '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	1044 ## metabolite logP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1045 'metabolite/predicted_properties/property' => sub {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1046
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1047 my ($kind, $source, $value ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1048
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1049 if (defined $_->children ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1050 foreach my $field ($_->children) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1051 if ( $field->name eq 'kind') { $kind = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1052 elsif ( $field->name eq 'source') { $source = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1053 elsif ( $field->name eq 'value') { $value = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1054
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1055 if (defined $source ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1056 if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1057 $metabocard_features{$id}{'metabolite_logp'} = $value ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1058 $metabocard_features{$id}{'STATUS'} = 'EXISTING' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1059 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1060 ($kind, $source, $value ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1061 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1062 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1063 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1064 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1065 },
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1066 pretty_print => 'indented',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1067 error_context => 1, $query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1068 );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1069
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1070 # $twig->print;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1071 $twig->purge ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1072
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1073 # if (!$@) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1074 #
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1075 # }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1076 # else {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1077 # warn $@ ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1078 # }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1079 } ## ELSIF success
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1080 } # END if defined URL
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1081 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1082 warn "\tThe hmdb metabocard url is not defined\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1083 last;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1084 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1085 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1086 } ## End IF defined ids
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1087 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1088 warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1089 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1090
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1091 # print Dumper %metabocard_features ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1092 return (\%metabocard_features) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1093 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1094 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1095
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1096
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1097 =head2 METHOD map_suppl_data_on_hmdb_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1098
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1099 ## 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	1100 ## Input : $results, $features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1101 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1102 ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1103
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1104 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1105 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1106 sub map_suppl_data_on_hmdb_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1107 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1108 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1109 my ( $results, $features ) = @_;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1110 my ( @moreResults ) = ( () ) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1111
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1112 foreach my $result (@{$results}) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1113
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1114 my @newResult = () ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1115
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1116 foreach my $entry (@{$result}) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1117
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1118 if ( ($entry->{'ENTRY_ENTRY_ID'}) and ($entry->{'ENTRY_ENTRY_ID'} ne '' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1119
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1120 my $current_id = $entry->{'ENTRY_ENTRY_ID'} ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1121 my $newCompletedEntry = $entry ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1122
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1123 ## If the id exists in feature hash and its status is not NOT_EXISTING
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1124 if ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'EXISTING' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1125
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1126 ## Metabolite NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1127 if (defined $features->{"$current_id"}{'metabolite_name'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1128 $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1129 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1130 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1131 $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1132 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1133 ## Metabolite INCHI
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1134 if (defined $features->{"$current_id"}{'metabolite_inchi'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1135 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1136 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1137 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1138 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NA' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1139 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1140 ## Metabolite LOGP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1141 if (defined $features->{"$current_id"}{'metabolite_logp'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1142 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1143 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1144 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1145 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NA' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1146 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1147 push (@newResult, $newCompletedEntry) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1148 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1149 elsif ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'NOT_EXISTING' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1150 $newCompletedEntry = undef ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1151 next ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1152
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1153 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1154 ## In cas no features are given
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1155 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1156 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NONEDATA' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1157 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NONEDATA' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1158 push (@newResult, $newCompletedEntry) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1159 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1160 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1161 } ## END FOREACH ENTRIES
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1162
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1163 push (@moreResults, \@newResult) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1164
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1165 } ## END FOREACH RESULT
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1166
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1167 return (\@moreResults) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1168 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1169 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1170
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1171
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1172 =head2 METHOD set_html_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1173
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1174 ## Description : initializes and build the tbody object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1175 ## Input : $nb_pages, $nb_items_per_page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1176 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1177 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1178
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1179 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1180 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1181 sub set_html_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1182 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1183 my ( $nb_pages, $nb_items_per_page ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1184
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1185 my ( @tbody_object ) = ( ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1186
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1187 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1188
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1189 my %pages = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1190 # tbody feature
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1191 PAGE_NB => $i,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1192 MASSES => [], ## end MASSES
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1193 ) ; ## end TBODY N
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1194 push (@tbody_object, \%pages) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1195 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1196 return(\@tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1197 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1198 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1199
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1200 =head2 METHOD add_mz_to_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1201
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1202 ## Description : initializes and build the mz object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1203 ## Input : $tbody_object, $nb_items_per_page, $mz_list
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1204 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1205 ## 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	1206
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1207 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1208 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1209 sub add_mz_to_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1210 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1211 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1212
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1213 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1214
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1215 foreach my $page ( @{$tbody_object} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1216
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1217 my @colors = ('white', 'green') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1218 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1219
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1220 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1221 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1222 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1223 $current_index = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1224 last ; ##
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1225 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1226 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1227 $current_index++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1228 if ( $icolor > 1 ) { $icolor = 0 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1229
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1230 if ( exists $mz_list->[$mz_index] ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1231
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1232 my %mz = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1233 # mass feature
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1234 MASSES_ID_QUERY => $ids_list->[$mz_index],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1235 MASSES_MZ_QUERY => $mz_list->[$mz_index],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1236 MZ_COLOR => $colors[$icolor],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1237 MASSES_NB => $mz_index+1,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1238 ENTRIES => [] ,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1239 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1240 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1241 # Html attr for mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1242 $icolor++ ;
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 $mz_index++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1246 } ## foreach mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1247
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1248 $current_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1249 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1250 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1251 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1252 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1253
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1254 =head2 METHOD add_entries_to_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1255
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1256 ## Description : initializes and build the entries object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1257 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1258 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1259 ## 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	1260
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1261 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1262 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1263 sub add_entries_to_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1264 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1265 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1266 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1267
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1268 my $index_page = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1269 my $index_mz_continous = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1270
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1271 foreach my $page (@{$tbody_object}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1272
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1273 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1274
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1275 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1276
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1277 my $index_entry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1278
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1279 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1280 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1281 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1282
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1283 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1284 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1285 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1286 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1287 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	1288 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1289
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1290 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1291
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1292 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1293
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1294 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1295 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1296 ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1297 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1298 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1299 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1300 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1301 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1302 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1303 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1304 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1305 ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1306 ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1307 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1308
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1309 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1310 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1311 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1312 $index_entry++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1313 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1314 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1315 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1316 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1317 ENTRY_ENTRY_NAME => 'UNKNOWN',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1318 ENTRY_ENTRY_ID => 'NONE',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1319 ENTRY_ENTRY_ID2 => '',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1320 ENTRY_FORMULA => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1321 ENTRY_CPD_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1322 ENTRY_ADDUCT => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1323 ENTRY_ADDUCT_TYPE => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1324 ENTRY_ADDUCT_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1325 ENTRY_DELTA => 0,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1326 ENTRY_ENTRY_INCHI => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1327 ENTRY_ENTRY_LOGP => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1328 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1329 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1330 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1331 $index_mz ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1332 $index_mz_continous ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1333 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1334 $index_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1335 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1336 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1337 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1338 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1339
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1340 =head2 METHOD write_html_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1341
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1342 ## Description : prepare and write the html output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1343 ## Input : $html_file_name, $html_object, $html_template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1344 ## Output : $html_file_name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1345 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1346
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1347 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1348 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1349 sub write_html_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1350 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1351 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1352 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1353
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1354 my $html_file = $$html_file_name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1355
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1356 if ( defined $html_file ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1357 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1358
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1359 if (-e $html_template) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1360 my $ohtml = HTML::Template->new(filename => $html_template);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1361 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1362 $ohtml->param( CONDITIONS => $search_condition ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1363 $ohtml->param( PAGES_NB => $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1364 $ohtml->param( PAGES => $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1365 print HTML $ohtml->output ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1366 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1367 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1368 croak "Can't fill any html output : No template available ($html_template)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1369 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1370
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1371 close (HTML) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1372 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1373 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1374 croak "No output file name available to write HTML file\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1375 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1376 return(\$html_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1377 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1378 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1379
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1380 =head2 METHOD set_lm_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1381
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1382 ## Description : build the hmdb_row under its ref form
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1383 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1384 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1385 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1386
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1387 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1388 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1389 sub set_lm_matrix_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1390 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1391 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1392 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1393
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1394 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1395
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1396 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1397 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1398 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1399 push @hmdb_matrix, \@headers ;
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 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1403
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1404 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1405
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1406 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1407 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1408 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1409
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1410 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1411 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1412
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1413 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1414
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1415 foreach my $entry (@{ $entries->[$index_mz] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1416
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1417 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1418 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1419 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1420 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1421
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1422 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1423
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1424 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1425
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1426 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1427 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1428 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1429
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1430 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1431 ## entry1=VAR1::VAR2::VAR3::VAR4\|entry2=VAR1::VAR2::VAR3::VAR4\|...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1432 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1433 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'\|' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1434 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1435
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1436 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1437 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1438 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1439 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1440 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1441 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1442 push (@hmdb_matrix, \@clusters) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1443 $index_mz++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1444 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1445 return(\@hmdb_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1446 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1447 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1448
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1449 =head2 METHOD set_hmdb_matrix_object_with_ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1450
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1451 ## Description : build the hmdb_row under its ref form (IDS only)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1452 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1453 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1454 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1455
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1456 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1457 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1458 sub set_hmdb_matrix_object_with_ids {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1459 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1460 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1461 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1462
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1463 # print Dumper $entries ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1464
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1465 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1466
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1467 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1468 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1469
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1470 ## redefined the header hmdb(delta::name::mz::formula::adduct::id)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1471 $header = 'hmdb(delta::name::mz::formula::adduct::id)' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1472 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1473 push @hmdb_matrix, \@headers ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1474 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1475
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1476 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1477
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1478 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1479
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1480 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1481 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1482 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1483
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1484 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1485 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1486
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1487 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1488
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1489 foreach my $entry (@{ $entries->[$index_mz] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1490
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1491 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1492 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1493 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1494 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1495
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1496 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1497
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1498 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1499 ##
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1500
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1501 my ($hmdb_name, $hmdb_id, $hmdb_formula, $hmdb_cpd_mz, $hmdb_adduct, $hmdb_delta) = (undef, undef, undef, undef, undef, undef) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1502
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1503 if ($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	1504 else { $hmdb_name = 'UNKNOWN' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1505
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1506 if ($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	1507 else { $hmdb_id = 0 ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1508
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1509 if ($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	1510 else { $hmdb_formula = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1511
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1512 if ($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	1513 else { $hmdb_cpd_mz = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1514
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1515 if ($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	1516 else { $hmdb_adduct = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1517
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1518 if ($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	1519 else { $hmdb_delta = 0 ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1520
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1521
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1522 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1523 ## 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	1524 my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1525
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1526 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1527 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' \| ' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1528 else { $cluster_col .= $entry ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1529
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1530 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1531 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1532 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1533 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1534 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1535 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1536 push (@hmdb_matrix, \@clusters) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1537 $index_mz++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1538 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1539 return(\@hmdb_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1540 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1541 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1542
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1543 =head2 METHOD add_lm_matrix_to_input_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1544
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1545 ## Description : build a full matrix (input + lm column)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1546 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1547 ## Output : $output_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1548 ## 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	1549
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1550 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1551 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1552 sub add_lm_matrix_to_input_matrix {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1553 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1554 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1555 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1556
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1557 my @output_matrix_object = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1558 my $index_row = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1559 my $line = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1560
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1561 foreach my $row ( @{$input_matrix_object} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1562 my @init_row = @{$row} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1563 $line++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1564
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1565 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1566 push (@output_matrix_object, \@init_row) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1567 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1568 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1569
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1570 if ( $lm_matrix_object->[$index_row] ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1571 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1572
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1573 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1574 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1575
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1576 push (@init_row, $lm_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1577 $index_row++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1578 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1579 push (@output_matrix_object, \@init_row) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1580 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1581 return(\@output_matrix_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1582 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1583 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1584
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1585 =head2 METHOD write_csv_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1586
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1587 ## Description : prepare and write csv output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1588 ## Input : $csv_file, $rows
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1589 ## Output : $csv_file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1590 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1591
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1592 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1593 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1594 sub write_csv_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1595 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1596 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1597 my ( $csv_file, $rows ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1598
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1599 # my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1600 my $ocsv = lib::csv::new() ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1601 my $csv = $ocsv->get_csv_object("\t") ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1602 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1603
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1604 return($csv_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1605 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1606 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1607
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1608 =head2 METHOD write_csv_one_mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1609
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1610 ## Description : print a cvs file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1611 ## Input : $masses, $ids, $results, $file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1612 ## Output : N/A
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1613 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1614
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1615 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1616 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1617 sub write_csv_one_mass {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1618 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1619 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1620 my ( $masses, $ids, $results, $file, ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1621
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1622 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1623 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	1624
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1625 my $i = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1626
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1627 foreach my $id (@{$ids}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1628 my $mass = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1629 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1630 else { last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1631
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1632 if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1633
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1634 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1635 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1636 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1637
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1638 foreach my $entry (@{$results->[$i]}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1639 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1640 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1641 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1642 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1643 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1644 # print "\n-----------------------" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1645 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1646 # print "-------------------------$check_rebond\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1647 # print Dumper @anti_redondant ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1648 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1649
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1650 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1651
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1652 print CSV "$id\t$mass\t" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1653
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1654 ## print delta
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1655 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1656 else { print CSV "0\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1657
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1658 ## print cpd name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1659 if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1660 else { print CSV "UNKNOWN\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1661
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1662 ## print cpd mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1663 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1664 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1665
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1666 ## print cpd formula
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1667 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1668 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1669
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1670 ## print adduct
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1671 if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1672 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1673
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1674 ## print adduct mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1675 if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1676 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1677
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1678 ## print cpd id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1679 if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1680 else { print CSV "N/A\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1681 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1682 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1683 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1684 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1685 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	1686 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1687 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1688 $i++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1689 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1690 close(CSV) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1691 return() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1692 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1693 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1694
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1695 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1696
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1697
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1698 __END__
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1699
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1700 =head1 SUPPORT
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1701
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1702 You can find documentation for this module with the perldoc command.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1703
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1704 perldoc hmdb.pm
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1705
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1706 =head1 Exports
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1707
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1708 =over 4
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1709
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1710 =item :ALL is ...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1711
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1712 =back
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1713
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1714 =head1 AUTHOR
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1715
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1716 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1717
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1718 =head1 LICENSE
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1719
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1720 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	1721
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1722 =head1 VERSION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1723
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1724 version 1 : 06 / 06 / 2013
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1725
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1726 version 2 : 27 / 01 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1727
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1728 version 3 : 19 / 11 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1729
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1730 version 4 : 28 / 01 / 2016
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1731
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1732 version 5 : 02 / 11 /2016
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1733
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1734 =cut

Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate lib/hmdb.pm @ 29:29195cb5d378 draft default tip