hmdb_ms_search: lib/hmdb.pm annotate

annotate lib/hmdb.pm @ 23:2d8a310e86ce draft

Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx

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

rev	line source
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1 package lib::hmdb ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	2
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	3 use strict;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	4 use warnings ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	5 use Exporter ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	6 use Carp ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	7
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	8 use LWP::Simple;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	9 use LWP::UserAgent;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	10 use WWW::Mechanize qw();
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	11 use URI::URL;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	12 use SOAP::Lite;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	13 use Encode qw(encode_utf8);
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	14 use HTML::Template ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	15 use XML::Twig ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	16 use Text::CSV ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	17
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	18 use Data::Dumper ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	19
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	20 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	21
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	22 our $VERSION = "1.0";
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	23 our @ISA = qw(Exporter);
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	24 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	25 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	26
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	27 =head1 NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	28
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	29 My::Module - An example module
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	30
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	31 =head1 SYNOPSIS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	32
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	33 use My::Module;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	34 my $object = My::Module->new();
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	35 print $object->as_string;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	36
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	37 =head1 DESCRIPTION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	38
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	39 This module does not really exist, it
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	40 was made for the sole purpose of
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	41 demonstrating how POD works.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	42
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	43 =head1 METHODS
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	44
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	45 Methods are :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	46
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	47 =head2 METHOD new
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	48
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	49 ## Description : new
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	50 ## Input : $self
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	51 ## Ouput : bless $self ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	52 ## Usage : new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	53
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	54 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	55
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	56 sub new {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	57 ## Variables
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	58 my $self={};
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	59 bless($self) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	60 return $self ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	61 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	62 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	63
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	64
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	65 =head2 METHOD extract_sub_mz_lists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	66
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	67 ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	68 ## Input : $HMDB_LIMITS, $masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	69 ## Output : $sublists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	70 ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	71
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	72 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	73 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	74 sub extract_sub_mz_lists {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	75 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	76 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	77 my ( $masses, $HMDB_LIMITS ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	78
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	79 my ( @sublists, @sublist ) = ( (), () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	80 my $nb_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	81 my $nb_total_mzs = scalar(@{$masses}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	82
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	83 if ($nb_total_mzs == 0) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	84 die "The provided mzs list is empty" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	85 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	86
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	87 for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	88
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	89 if ( $nb_mz < $HMDB_LIMITS ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	90 if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	91 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	92 elsif ( $nb_mz == $HMDB_LIMITS ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	93 my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	94 $current_pos-- ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	95 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	96 if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	97 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	98 return(\@sublists) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	99 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	100 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	101
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	102 =head2 METHOD prepare_multi_masses_query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	103
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	104 ## Description : Generate the adapted format of the mz list for HMDB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	105 ## Input : $masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	106 ## Output : $hmdb_masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	107 ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	108
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	109 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	110 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	111 sub prepare_multi_masses_query {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	112 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	113 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	114 my ( $masses ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	115
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	116 my $hmdb_masses = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	117 my $sep = '%0D%0A' ; ## retour chariot encode
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	118 my ($nb_masses, $i) = (0, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	119
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	120 if ( defined $masses ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	121 my @masses = @{$masses} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	122 my $nb_masses = scalar ( @masses ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	123 if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; }
6 7ed37640fe2a planemo upload commit 4c72059b94b27eda2c0ee89bfc5f9bf4e3425dc5 fgiacomoni parents: 4 diff changeset	124 elsif ( $nb_masses >= 700 ) { croak "Your mass list is too long : HMDB allows maximum 700 query masses per request \n" ; } ## Del it --- temporary patch
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	125
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	126 foreach my $mass (@masses) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	127
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	128 if ($i < $nb_masses) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	129 $hmdb_masses .= $mass.$sep ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	130 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	131 elsif ( $i == $nb_masses ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	132 $hmdb_masses .= $mass ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	133 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	134 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	135 last ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	136 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	137 $i ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	138 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	139 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	140 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	141 croak "No mass list found \n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	142 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	143 return($hmdb_masses, $nb_masses) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	144 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	145 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	146
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	147
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	148 =head2 METHOD prepareAdductListFormat
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	149
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	150 ## Description : prepare a adduct list well formatted for https queries
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	151 ## Input : $adductString
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	152 ## Output : $formattedAdductString
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	153 ## Usage : my ( $formattedAdductString ) = prepareAdductListFormat ( $adductString ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	154
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	155 =cut
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	156 ## START of SUB
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	157 sub prepareAdductListFormat {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	158 ## Retrieve Values
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	159 my $self = shift ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	160 my ( $adductString ) = @_;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	161 my ( $formattedAdductString, $nbAdducts ) = ( undef, 0 ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	162
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	163 ## Formatting is converting [+] in %2B, [-] as - and [,] in converted space as 'M%2BH%202M%2BH' for 'M+H,2M+2H'
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	164 # print "\t$adductString ..." ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	165
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	166 if (defined $adductString) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	167
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	168 ## counting selected adducts
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	169 $nbAdducts = scalar( my @adducts = ( split (/,/, $adductString) ) ) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	170
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	171 ## Converting string into http post format
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	172 $adductString =~ s/\+/%2B/g ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	173 $adductString =~ s/,/%20/g ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	174 $formattedAdductString = $adductString ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	175 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	176 else {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	177 warn "\t[WARN]the adduct type is not defined...It will set to 'Unknown'\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	178 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	179
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	180 # print "->$formattedAdductString\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	181
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	182 return ($formattedAdductString, $nbAdducts) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	183 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	184 ### END of SUB
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	185
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	186 =head2 METHOD test_matches_from_hmdb_ua DEPRECATED
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	187
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	188 ## Description : [DEPRECATED]test a single query with tests parameters on hmdb - get the status of the complete server infra.
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	189 ## Input : none
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	190 ## Output : $status_line
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	191 ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	192
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	193 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	194 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	195 sub test_matches_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	196 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	197 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	198
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	199 my @page = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	200
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	201 my $ua = new LWP::UserAgent;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	202 $ua->agent("Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:64.0) Gecko/20100101 Firefox/64.0");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	203
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	204 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	205 my $header = ['Connection' => 'keep-alive', 'Content-Type' => 'application/x-www-form-urlencoded', 'Referer' => 'http://www.hmdb.ca/spectra/ms/search', 'Accept' => 'text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8'];
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	206
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	207 my $req = HTTP::Request->new('POST', $url, $header);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	208 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	209
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	210 ## Query format for HMDB 4.0
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	211 #"utf8=✓&authenticity_token=K1Ys7oyMKmVNm9n8p0jiTxBlh4G4OO0cqKZYnQKDCw0pM6zmm/CiBxv+/cXhuRsVFV98LLeAMJRN5dCyhIWlAA==&query_masses=175.01 238.19 420.16 780.32 956.25 1100.45&ms_search_ion_mode=positive&adduct_type[]=Unknown&tolerance=0.05&tolerance_units=Da&commit=Search"
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	212
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	213 $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV');
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	214 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	215 my $res = $ua->request($req);
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	216
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	217 print $res->as_string;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	218 my $status_line = $res->status_line ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	219 ($status_line) = ($status_line =~ /(\d+)/);
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	220
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	221 return (\$status_line) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	222 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	223 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	224
22 453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	225
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	226 =head2 METHOD checkHmdbUrlEntries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	227
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	228 ## Description : check a list of HMDB_IDs by testing what is the status of their uri (HTTP 200 or not)
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	229 ## Input : $urlRoot, $entries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	230 ## Output : $validEntries
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	231 ## Usage : my ( $validEntries ) = checkHmdbUrlEntries ( $entries ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	232
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	233 =cut
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	234 ## START of SUB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	235 sub checkHmdbUrlEntries {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	236 ## Retrieve Values
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	237 my $self = shift ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	238 my ( $urlRoot, $clusters, $maxQuery ) = @_;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	239 my ( @ValidResults, @validFeature ) = ( (), () ) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	240
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	241 foreach my $resultsByMass (@{$clusters}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	242 my $currentQuery = 0 ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	243 foreach my $feature (@{$resultsByMass}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	244
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	245 if ($feature->{ENTRY_ENTRY_ID}) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	246
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	247 my $url = $urlRoot.$feature->{ENTRY_ENTRY_ID} ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	248 if ( get($url)) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	249 $currentQuery ++ ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	250 if ($currentQuery > $maxQuery) {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	251 last ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	252 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	253 else {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	254 push (@validFeature, $feature) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	255 # print "Url is valid ($url) - - add to final results\n" ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	256 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	257 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	258 else {
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	259 # print "Url is NOT valid ($url) - - Deleting to final results\n" ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	260 next ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	261 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	262 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	263 } # END FOREACH FEATURE
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	264 my @tmp = @validFeature ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	265 push (@ValidResults, \@tmp) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	266 @validFeature = () ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	267 } # END FOREACH RESULTS
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	268
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	269 return (\@ValidResults) ;
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	270 }
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	271 ### END of SUB
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	272
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx" fgiacomoni parents: 21 diff changeset	273
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	274 =head2 METHOD testMatchesFromHmdbWithUA
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	275
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	276 ## 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	277 ## Input : none
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	278 ## Output : $status_line
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	279 ## Usage : my ( $status_line ) = testMatchesFromHmdbWithUA( ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	280
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	281 =cut
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	282 ## START of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	283 sub testMatchesFromHmdbWithUA {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	284 ## Retrieve Values
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	285 my $self = shift ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	286
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	287 my @page = () ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	288 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	289
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	290 my $mech = WWW::Mechanize->new(
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	291 # agent => 'wonderbot for W4M 1.01',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	292 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	293 autocheck => 0,
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	294 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	295
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	296 my $statusGetLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	297 my $statusPostLine = 0 ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	298 my $csrftoken = undef ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	299
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	300 #receiving cookies and authentication token (CFRS)
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	301 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	302 $statusGetLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	303
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	304 if ($statusGetLine == 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	305 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	306 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	307 $csrftoken = $1;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	308 print "\nTOKEN: $csrftoken\n" ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	309 $mech->add_header("X-CSRFToken", $csrftoken);
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	310 $mech->add_header('Host', 'specdb.wishartlab.com');
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	311 $mech->add_header('Connection', 'keep-alive');
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	312 $mech->add_header('Upgrade-Insecure-Requests', '1');
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	313 $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	314 $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	315 $mech->add_header('Accept-Encoding', 'gzip, deflate');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	316 # $mech->add_header('Content-Length', "300");
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	317 $mech->add_header('Origin', 'null');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	318 $mech->add_header('DNT', '1');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	319 $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	320 # $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	321 $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	322
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	323
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	324 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	325
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	326 ## POST test
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	327 my $top = 1 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	328 while ($statusPostLine != 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	329
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	330 # Fix a limit at 3 tries...
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	331 if ($top < 4) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	332 print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	333 eval {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	334 $mech->post(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	335 "http://specdb.wishartlab.com/ms/search.csv",
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	336 Content => 'utf8=TRUE&authenticity_token='.$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	337 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	338 } ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	339 # print Dumper $mech ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	340 $statusPostLine = $mech->status() ;
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	341 print "Status: $statusPostLine" ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	342 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	343 else {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	344 last ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	345 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	346 $top++ ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	347 }## End While
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	348 return (\$statusPostLine) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	349 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	350 ## END of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	351
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	352
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	353 =head2 METHOD testMatchesFromHmdb5WithUA
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	354
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	355 ## 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	356 ## Input : none
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	357 ## Output : $status_line
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	358 ## Usage : my ( $status_line ) = testMatchesFromHmdb5WithUA( ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	359
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	360 =cut
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	361 ## START of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	362 sub testMatchesFromHmdb5WithUA {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	363 ## Retrieve Values
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	364 my $self = shift ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	365
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	366 my $mech = WWW::Mechanize->new(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	367 agent => 'wonderbot for W4M 3.0',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	368 autocheck => 1,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	369 timeout => 2400,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	370 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	371
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	372 my $statusGetLine = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	373 my $statusPostLine = 0 ;
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 #receiving cookies and authentication token (CFRS)
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	376 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	377 $statusGetLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	378
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	379 if ($statusGetLine == 200 ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	380 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	381 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	382 my $csrftoken = $1;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	383 # print "\nTOKEN: $csrftoken\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	384 $mech->add_header("X-CSRFToken", $csrftoken);
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	385 $mech->add_header('Connection', 'keep-alive');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	386 $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	387 $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	388 $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	389 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	390
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	391
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	392 ## POST test
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	393 my $top = 1 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	394 while ($statusPostLine != 200 ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	395
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	396 # Fix a limit at 3 tries...
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	397 if ($top < 4) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	398 print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	399 eval {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	400 my $res = $mech->get(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	401 'https://hmdb.ca/spectra/ms/generate_csv.csv?'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	402 .'results%5Baction%5D=search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	403 .'&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	404 #.'&results%5Bauthenticity_token%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	405 .'&results%5Bccs_predictors%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	406 .'&results%5Bccs_tolerance%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	407 .'&results%5Bcommit%5D=Search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	408 .'&results%5Bcontroller%5D=specdb%2Fms'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	409 .'&results%5Bms_search_ion_mode%5D=positive'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	410 .'&results%5Bquery_masses%5D=125.0089'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	411 .'&results%5Btolerance%5D=0.001'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	412 .'&results%5Btolerance_units%5D=Da'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	413 .'&results%5Butf8%5D=%E2%9C%93'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	414
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	415 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	416 } ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	417 # print Dumper $mech ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	418 $statusPostLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	419 print "Status: $statusPostLine" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	420 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	421 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	422 last ;
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 $top++ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	425 }## End While
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	426 return (\$statusPostLine) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	427 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	428 ## END of SUB
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	429
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	430 =head2 METHOD check_state_from_hmdb_ua
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	431
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	432 ## Description : check the thhp status of hmdb and kill correctly the script if necessary.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	433 ## Input : $status
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	434 ## Output : none
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	435 ## Usage : check_state_from_hmdb_ua($status) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	436
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	437 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	438 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	439 sub check_state_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	440 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	441 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	442 my ($status) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	443
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	444 if (!defined $$status) {
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	445 croak "No https status is defined for the distant server" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	446 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	447 else {
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	448 unless ( $$status == 200 ) {
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	449 if ( $$status == 502 ) { croak "Bad Gateway (502): The HMDB server, while acting as a gateway or proxy, received an invalid response from the upstream server. The Hmdb tool is stopped with error." ; }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	450 if ( $$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	451 if ( $$status == 500 ) { croak "Internal Server Error (500): The HMDB server returns an unexpected internal server error. The Hmdb tool is stopped with error." ; }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	452 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	453 ## None supported http code error ##
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	454 croak "Internal Server Error $$status..." ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	455 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	456 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	457 if ( $$status == 200 ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	458 print "\tThe HMDB server returns that your request (connexion test) was fulfilled\n" ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	459 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	460 }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	461 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	462
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	463 return (1) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	464 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	465 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	466
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	467 =head2 METHOD get_matches_from_hmdb_ua DEPRECATED
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	468
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	469 ## 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	470 ## Input : $mass, $delta, $mode
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	471 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	472 ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	473
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	474 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	475 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	476 sub get_matches_from_hmdb_ua {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	477 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	478 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	479 my ( $masses, $delta, $mode ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	480
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	481 ## Added May, 2022
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	482 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	483 return ([], 500) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	484
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	485 my @page = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	486
8 97788e4bf3fc planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392-dirty fgiacomoni parents: 6 diff changeset	487 my $ua = LWP::UserAgent->new( keep_alive => 10 );
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	488 $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	489 $ua->timeout(2400) ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	490
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	491 # Cookies
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	492 # my $cookie = new HTTP::Cookies( ignore_discard => 1 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	493 # $ua->cookie_jar( $cookie );
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	494
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	495 # my $req = HTTP::Request->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	496 # POST => 'http://specdb.wishartlab.com/ms/search.csv');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	497
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	498 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	499 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	500 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	501 my $encoded_data = encode_utf8($data);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	502
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	503 my $req = HTTP::Request->new('POST', $url, $header, $encoded_data);
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	504
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	505 # $req->content_type('application/x-www-form-urlencoded');
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	506 $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	507 # print Dumper $req ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	508 my $res = $ua->request($req);
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	509 my $status_line = undef ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	510 print $res->as_string;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	511 if ($res->is_success) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	512 @page = split ( /\n/, $res->decoded_content ) ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	513 $status_line = 'OK' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	514 } else {
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	515 $status_line = $res->status_line ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	516 ($status_line) = ($status_line =~ /(\d+)/);
17 49f87ddb2c78 Master branch Updating - - Fxx fgiacomoni parents: 15 diff changeset	517 warn "\t[HMDB service issue !! the server returned a $status_line HTTP error]" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	518 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	519
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	520
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	521 return (\@page, $status_line) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	522 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	523 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	524
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	525 =head2 METHOD getMatchesFromHmdbWithUA
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	526
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	527 ## 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	528 ## Input : $mass, $delta, $mode, adducts
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	529 ## Output : $results
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	530 ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	531
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	532 =cut
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	533 ## START of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	534 sub getMatchesFromHmdbWithUA {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	535 ## Retrieve Values
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	536 my $self = shift ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	537 my ( $masses, $delta, $mode, $adducts ) = @_ ;
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	538
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	539 ## Added May, 2022
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	540 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	541 return ([], 500) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	542
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	543 my @page = () ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	544
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	545 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	546
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	547 my $mech = WWW::Mechanize->new(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	548 agent => 'wonderbot for W4M 1.01',
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	549 autocheck => 1,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	550 timeout => 2400,
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	551 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	552
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	553 my $statusGetLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	554 my $statusPostLine = 0 ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	555
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	556 #receiving cookies and authentication token (CFRS)
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	557 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	558 $statusGetLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	559
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	560 if ($statusGetLine == 200 ) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	561 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	562 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	563 my $csrftoken = $1;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	564 # print "\nTOKEN: $csrftoken\n" ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	565 $mech->add_header("X-CSRFToken", $csrftoken);
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	566 $mech->add_header('Connection', 'keep-alive');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	567 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	568 $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	569 $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	570 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	571 ## adduct format is adduct_type=M%2BH%202M%2BH
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	572
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	573 if ( (!defined $adducts) or ( $adducts eq '') ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	574 $adducts = 'Unknown' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	575 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	576
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	577 my $res = $mech->post(
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	578 "http://specdb.wishartlab.com/ms/search.csv",
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	579 Content => 'utf8=TRUE&mode='
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	580 .$mode.'&adduct_type='
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	581 .$adducts.'&query_masses='
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	582 .$masses.'&tolerance='
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	583 .$delta.'&database=HMDB&commit=Download Results As CSV'
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	584 );
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	585
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	586 if ($mech->success) {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	587 @page = split ( /\n/, $res->decoded_content ) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	588 $statusPostLine = 'OK' ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	589 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	590 else {
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	591 $statusPostLine = $mech->status() ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	592 warn "\t[HMDB service issue !! the server returned a $statusPostLine HTTP error]" ;
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 # print Dumper $res->decoded_content ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	596
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	597 return (\@page, $statusPostLine) ;
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	598 }
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	599 ## END of SUB
b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	600
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	601 =head2 METHOD getMatchesFromHmdb5WithUA
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	602
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	603 ## 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	604 ## Input : $mass, $delta, $mode, adducts
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	605 ## Output : $results
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	606 ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	607
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	608 =cut
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	609 ## START of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	610 sub getMatchesFromHmdb5WithUA {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	611 ## Retrieve Values
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	612 my $self = shift ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	613 my ( $masses, $delta, $mode, $adducts ) = @_ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	614
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	615 my @page = () ;
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 #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	618
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	619 my $mech = WWW::Mechanize->new(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	620 agent => 'wonderbot for W4M 3.0',
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	621 autocheck => 1,
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	622 timeout => 2400,
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
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	625 my $statusGetLine = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	626 my $statusPostLine = 0 ;
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 #receiving cookies and authentication token (CFRS)
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	629 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	630 $statusGetLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	631
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	632 if ($statusGetLine == 200 ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	633 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	634 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	635 my $csrftoken = $1;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	636 # print "\nTOKEN: $csrftoken\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	637 $mech->add_header("X-CSRFToken", $csrftoken);
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	638 $mech->add_header('Connection', 'keep-alive');
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	639 $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	640 $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	641 $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	642 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	643 ## adduct format is adduct_type=M%2BH%202M%2BH
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	644
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	645 if ( (!defined $adducts) or ( $adducts eq '') ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	646 $adducts = 'Unknown' ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	647 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	648
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	649 my $res = $mech->get(
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	650 'https://hmdb.ca/spectra/ms/generate_csv.csv?'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	651 .'results%5Baction%5D=search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	652 .'&results%5Badduct_type%5D%5B%5D='.$adducts
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	653 #.'&results%5Bauthenticity_token%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	654 .'&results%5Bccs_predictors%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	655 .'&results%5Bccs_tolerance%5D='
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	656 .'&results%5Bcommit%5D=Search'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	657 .'&results%5Bcontroller%5D=specdb%2Fms'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	658 .'&results%5Bms_search_ion_mode%5D='.$mode
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	659 .'&results%5Bquery_masses%5D='.$masses
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	660 .'&results%5Btolerance%5D='.$delta
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	661 .'&results%5Btolerance_units%5D=Da'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	662 .'&results%5Butf8%5D=%E2%9C%93'
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	663
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	664 );
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	665 $statusGetLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	666
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	667 if ($mech->success) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	668 @page = split ( /\n/, $res->decoded_content ) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	669 $statusPostLine = 'OK' ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	670 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	671 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	672 $statusPostLine = $mech->status() ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	673 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	674 }
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 # print Dumper $res->decoded_content ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	677
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	678 return (\@page, $statusPostLine) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	679 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	680 ## END of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	681
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 =head2 METHOD parseHmdb5CSVResults
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	684
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	685 ## 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	686 ## Input : $csv
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	687 ## Output : $results
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	688 ## Usage : my ( $results ) = parseHmdb5CSVResults( $csv ) ;
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 =cut
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	691 ## START of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	692 sub parseHmdb5CSVResults {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	693 ## Retrieve Values
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	694 my $self = shift ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	695 my ( $csv, $masses, $max_query ) = @_ ;
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 my $test = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	698 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	699
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	700 my %result_by_entry = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	701 my %features = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	702
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	703 # print Dumper $csv ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	704 # print Dumper $masses ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	705 # print Dumper $max_query ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	706
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	707 foreach my $line (@{$csv}) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	708 ## NEW HMDB format V5.0 - May2022
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	709 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	710 #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	711
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	712 if ( $line =~ /(\d+\.\d+),(\w+),(.),(\w+),(\d+\.\d+),([\w\|n\/a\|\s+]+)\s,(\+\|\-),(\d+\.\d+),(\d+),(\d*)/ ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	713 print "$line\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	714 #if ( $line =~ /(\d+\.\d+),(\w+),(.),([\w\|n\/a\|\s+]+)\s,(\w+),(\d+\.\d+),(.*),(\+\|\-),(\d+\.\d+),(\d+)/ ) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	715 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	716
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	717 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	718
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	719 $features{ENTRY_ENTRY_ID} = $entry[1] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	720 $features{ENTRY_ENTRY_NAME} = $entry[2] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	721 $features{ENTRY_FORMULA} = $entry[3] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	722 $features{ENTRY_CPD_MZ} = $entry[4] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	723 $features{ENTRY_ADDUCT} = $entry[5] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	724 $features{ENTRY_ADDUCT_TYPE} = $entry[6] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	725 $features{ENTRY_ADDUCT_MZ} = $entry[7] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	726 $features{ENTRY_DELTA} = $entry[8] ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	727
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	728 my %temp = %features ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	729 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
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 # elsif ($line =~ /(\d+\.\d+)/) { #
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	732 # ## 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	733 # ## 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	734 # ## 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	735 # ## 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	736 # ## 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	737 # }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	738 # else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	739 #
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	740 # 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	741 # }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	742 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	743 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	744 print "Header detected...Parsing is starting...\n" ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	745 next ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	746 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	747 } ## end foreach
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	748
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	749 ## 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	750 my @results = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	751 foreach (@{$masses}) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	752 if ($result_by_entry{$_}) {
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 ## 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	755 my @temp_entries = @{$result_by_entry{$_}} ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	756 my @temp_cut = () ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	757 my $current_query = 0 ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	758 foreach (@temp_entries) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	759 $current_query ++ ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	760 if ($current_query > $max_query) {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	761 last ;
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 else {
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	764 push (@temp_cut, $_) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	765 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	766 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	767 push (@results, \@temp_cut) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	768 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	769 else { push (@results, [] ) ; } ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	770
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	771 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	772 return(\@results) ;
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	773 }
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	774 ## END of SUB
2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	775
20 b5a1d5e43685 Master branch Updating - - Fxx fgiacomoni parents: 17 diff changeset	776
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	777 =head2 METHOD parse_hmdb_csv_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	778
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	779 ## Description : [DEPRECATED] parse the csv results and get data
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	780 ## Input : $csv
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	781 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	782 ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	783
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	784 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	785 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	786 sub parse_hmdb_csv_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	787 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	788 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	789 my ( $csv, $masses, $max_query ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	790
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	791 my $test = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	792 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	793
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	794 my %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	795 my %features = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	796
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	797 # print Dumper $csv ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	798 # print Dumper $masses ;
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	799 # print Dumper $max_query ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	800
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	801 foreach my $line (@{$csv}) {
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	802 ## NEW HMDB format V4.0 - dec2017
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	803 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	804
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	805 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	806 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	807
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	808 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	809
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	810 $features{ENTRY_ENTRY_ID} = $entry[1] ;
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	811 $features{ENTRY_ENTRY_NAME} = $entry[2] ;
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	812 $features{ENTRY_FORMULA} = $entry[4] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	813 $features{ENTRY_CPD_MZ} = $entry[5] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	814 $features{ENTRY_ADDUCT} = $entry[6] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	815 $features{ENTRY_ADDUCT_TYPE} = $entry[7] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	816 $features{ENTRY_ADDUCT_MZ} = $entry[8] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	817 $features{ENTRY_DELTA} = $entry[9] ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	818
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	819 my %temp = %features ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	820 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	821 }
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	822 # elsif ($line =~ /(\d+\.\d+)/) { #
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	823 # ## 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	824 # ## 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	825 # ## 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	826 # ## 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	827 # ## 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	828 # }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	829 # else {
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	830 #
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	831 # warn "The parsed line ($line) does not match your pattern\n " ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	832 # }
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	833 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	834 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	835 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	836 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	837 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	838
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	839 ## manage per query_mzs (keep query masses order by array)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	840 my @results = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	841 foreach (@{$masses}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	842 if ($result_by_entry{$_}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	843
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	844 ## cut all entries > $max_query - all entries were already sorted...by hmdb
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	845 my @temp_entries = @{$result_by_entry{$_}} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	846 my @temp_cut = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	847 my $current_query = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	848 foreach (@temp_entries) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	849 $current_query ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	850 if ($current_query > $max_query) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	851 last ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	852 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	853 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	854 push (@temp_cut, $_) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	855 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	856 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	857 push (@results, \@temp_cut) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	858 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	859 else { push (@results, [] ) ; } ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	860
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	861 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	862 return(\@results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	863 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	864 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	865
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	866 =head2 METHOD parse_hmdb_page_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	867
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	868 ## Description : [DEPRECATED] old HMDB html page parser
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	869 ## Input : $page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	870 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	871 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	872
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	873 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	874 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	875 sub parse_hmdb_page_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	876 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	877 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	878 my ( $page ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	879
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	880 my @results = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	881 my ($catch_table, $catch_name) = (0, 0) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	882 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	883
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	884 if ( defined $page ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	885
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	886 my @page = @{$page} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	887 my $ID = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	888 my @result_by_mz = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	889 my %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	890
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	891 foreach my $line (@page) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	892
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	893 #Section de la page contenant les resultat
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	894 if( $line =~/<table>/ ) { $catch_table = 1 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	895
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	896 ## Si il existe un resultat :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	897 if($catch_table == 1) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	898
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	899 #Id de la molecule, et creation du lien
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	900 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	901 $ID = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	902 $catch_name = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	903 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	904 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	905 #Nom de la molecule ONLY!!
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	906 if ( $catch_name == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	907
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	908 if( $line =~ /<td>(.+)<\/td>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	909
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	910 if ( !defined $name ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	911 $name = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	912 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	913 $result_by_entry{'ENTRY_NAME'} = $name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	914 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	915 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	916 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	917 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	918 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	919 if ( !defined $delta ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	920 $delta = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	921 $result_by_entry{'ENTRY_DELTA'} = $delta ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	922 $catch_name = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	923 my %tmp = %result_by_entry ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	924 push (@result_by_mz, \%tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	925 %result_by_entry = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	926 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	927 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	928 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	929 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	930 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	931 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	932 #Fin de la section contenant les resultats
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	933 if( $line =~ /<\/table>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	934 $catch_table = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	935 my @Tmp = @result_by_mz ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	936 push(@results, \@Tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	937 @result_by_mz = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	938 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	939 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	940 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	941 return(\@results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	942 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	943 ## END of SUB
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 =head2 METHOD get_unik_ids_from_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	947
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	948 ## Description : get all unik ids from the hmdb result object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	949 ## Input : $results
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	950 ## Output : $ids, $idsNumber
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	951 ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	952
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	953 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	954 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	955 sub get_unik_ids_from_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	956 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	957 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	958 my ( $results ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	959 my ( %ids ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	960
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	961 foreach my $result (@{$results}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	962
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	963 foreach my $entries (@{$result}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	964
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	965 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	966 $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	967 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	968 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	969 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	970 my $idsNumber = keys %ids ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	971 return (\%ids, $idsNumber) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	972 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	973 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	974
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	975
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	976
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	977 =head2 METHOD get_hmdb_metabocard_from_id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	978
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	979 ## Description : get a metabocard (xml format from an ID on HMDB)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	980 ## Input : $ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	981 ## Output : $metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	982 ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	983
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	984 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	985 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	986 sub get_hmdb_metabocard_from_id {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	987 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	988 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	989 my ( $ids, $hmdb_url ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	990 my ( %metabocard_features ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	991 my $query = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	992
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	993 ## structure %metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	994 # metabolite_id = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	995 # 'metabolite_name' => '__name__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	996 # 'metabolite_inchi' => '__inchi__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	997 # 'metabolite_logp' => '__logp-ALOGPS__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	998 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	999 # )
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1000
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1001
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1002 if( (defined $ids) and ($ids > 0 ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1003
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1004 foreach my $id (keys %{$ids}) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1005 print "$id...\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1006 my $twig = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1007
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1008 if (defined $hmdb_url) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1009 $query = $hmdb_url.$id.'.xml' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1010
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1011 ## test the header if exists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1012 my $response = head($query) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1013
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1014 if (!defined $response) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1015 $metabocard_features{$id}{'STATUS'} = 'NOT_EXISTING' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1016 $metabocard_features{$id}{'metabolite_name'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1017 $metabocard_features{$id}{'metabolite_inchi'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1018 $metabocard_features{$id}{'metabolite_logp'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1019 ## 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	1020 } ## IF error
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1021 elsif ( $response->is_success ) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1022
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1023 $twig = XML::Twig->nparse_ppe(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1024
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1025 twig_handlers => {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1026 # metabolite name
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1027 '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	1028 # metabolite inchi
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1029 '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	1030 ## metabolite logP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1031 'metabolite/predicted_properties/property' => sub {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1032
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1033 my ($kind, $source, $value ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1034
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1035 if (defined $_->children ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1036 foreach my $field ($_->children) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1037 if ( $field->name eq 'kind') { $kind = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1038 elsif ( $field->name eq 'source') { $source = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1039 elsif ( $field->name eq 'value') { $value = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1040
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1041 if (defined $source ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1042 if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1043 $metabocard_features{$id}{'metabolite_logp'} = $value ;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1044 $metabocard_features{$id}{'STATUS'} = 'EXISTING' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1045 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1046 ($kind, $source, $value ) = ( undef, undef, undef ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1047 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1048 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1049 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1050 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1051 },
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1052 pretty_print => 'indented',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1053 error_context => 1, $query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1054 );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1055
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1056 # $twig->print;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1057 $twig->purge ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1058
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1059 # if (!$@) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1060 #
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1061 # }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1062 # else {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1063 # warn $@ ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1064 # }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1065 } ## ELSIF success
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1066 } # END if defined URL
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1067 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1068 warn "\tThe hmdb metabocard url is not defined\n" ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1069 last;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1070 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1071 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1072 } ## End IF defined ids
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1073 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1074 warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1075 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1076
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1077 # print Dumper %metabocard_features ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1078 return (\%metabocard_features) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1079 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1080 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1081
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1082
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1083 =head2 METHOD map_suppl_data_on_hmdb_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1084
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1085 ## 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	1086 ## Input : $results, $features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1087 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1088 ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1089
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1090 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1091 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1092 sub map_suppl_data_on_hmdb_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1093 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1094 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1095 my ( $results, $features ) = @_;
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1096 my ( @moreResults ) = ( () ) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1097
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1098 foreach my $result (@{$results}) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1099
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1100 my @newResult = () ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1101
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1102 foreach my $entry (@{$result}) {
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1103
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1104 if ( ($entry->{'ENTRY_ENTRY_ID'}) and ($entry->{'ENTRY_ENTRY_ID'} ne '' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1105
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1106 my $current_id = $entry->{'ENTRY_ENTRY_ID'} ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1107 my $newCompletedEntry = $entry ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1108
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1109 ## If the id exists in feature hash and its status is not NOT_EXISTING
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1110 if ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'EXISTING' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1111
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1112 ## Metabolite NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1113 if (defined $features->{"$current_id"}{'metabolite_name'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1114 $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1115 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1116 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1117 $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1118 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1119 ## Metabolite INCHI
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1120 if (defined $features->{"$current_id"}{'metabolite_inchi'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1121 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1122 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1123 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1124 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NA' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1125 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1126 ## Metabolite LOGP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1127 if (defined $features->{"$current_id"}{'metabolite_logp'} ) {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1128 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'}
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_LOGP'} = 'NA' ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1132 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1133 push (@newResult, $newCompletedEntry) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1134 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1135 elsif ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'NOT_EXISTING' ) ) {
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1136 $newCompletedEntry = undef ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1137 next ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1138
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1139 }
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1140 ## In cas no features are given
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1141 else {
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1142 $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NONEDATA' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1143 $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NONEDATA' ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1144 push (@newResult, $newCompletedEntry) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1145 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1146 }
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1147 } ## END FOREACH ENTRIES
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1148
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1149 push (@moreResults, \@newResult) ;
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1150
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1151 } ## END FOREACH RESULT
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1152
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 20 diff changeset	1153 return (\@moreResults) ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1154 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1155 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1156
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1157
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1158 =head2 METHOD set_html_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1159
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1160 ## Description : initializes and build the tbody object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1161 ## Input : $nb_pages, $nb_items_per_page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1162 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1163 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1164
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1165 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1166 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1167 sub set_html_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1168 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1169 my ( $nb_pages, $nb_items_per_page ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1170
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1171 my ( @tbody_object ) = ( ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1172
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1173 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1174
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1175 my %pages = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1176 # tbody feature
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1177 PAGE_NB => $i,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1178 MASSES => [], ## end MASSES
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1179 ) ; ## end TBODY N
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1180 push (@tbody_object, \%pages) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1181 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1182 return(\@tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1183 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1184 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1185
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1186 =head2 METHOD add_mz_to_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1187
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1188 ## Description : initializes and build the mz object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1189 ## Input : $tbody_object, $nb_items_per_page, $mz_list
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1190 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1191 ## 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	1192
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1193 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1194 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1195 sub add_mz_to_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1196 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1197 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1198
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1199 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1200
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1201 foreach my $page ( @{$tbody_object} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1202
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1203 my @colors = ('white', 'green') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1204 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1205
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1206 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1207 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1208 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1209 $current_index = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1210 last ; ##
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1211 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1212 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1213 $current_index++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1214 if ( $icolor > 1 ) { $icolor = 0 ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1215
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1216 if ( exists $mz_list->[$mz_index] ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1217
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1218 my %mz = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1219 # mass feature
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1220 MASSES_ID_QUERY => $ids_list->[$mz_index],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1221 MASSES_MZ_QUERY => $mz_list->[$mz_index],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1222 MZ_COLOR => $colors[$icolor],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1223 MASSES_NB => $mz_index+1,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1224 ENTRIES => [] ,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1225 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1226 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1227 # Html attr for mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1228 $icolor++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1229 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1230 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1231 $mz_index++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1232 } ## foreach mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1233
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1234 $current_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1235 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1236 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1237 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1238 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1239
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1240 =head2 METHOD add_entries_to_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1241
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1242 ## Description : initializes and build the entries object (perl array) needed to html template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1243 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1244 ## Output : $tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1245 ## 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	1246
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1247 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1248 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1249 sub add_entries_to_tbody_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1250 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1251 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1252 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1253
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1254 my $index_page = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1255 my $index_mz_continous = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1256
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1257 foreach my $page (@{$tbody_object}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1258
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1259 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1260
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1261 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1262
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1263 my $index_entry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1264
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1265 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1266 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1267 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1268
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1269 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1270 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1271 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1272 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1273 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	1274 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1275
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1276 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1277
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1278 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1279
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1280 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1281 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1282 ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1283 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1284 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1285 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1286 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1287 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1288 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1289 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1290 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1291 ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1292 ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1293 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1294
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1295 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1296 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1297 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1298 $index_entry++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1299 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1300 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1301 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1302 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1303 ENTRY_ENTRY_NAME => 'UNKNOWN',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1304 ENTRY_ENTRY_ID => 'NONE',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1305 ENTRY_ENTRY_ID2 => '',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1306 ENTRY_FORMULA => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1307 ENTRY_CPD_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1308 ENTRY_ADDUCT => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1309 ENTRY_ADDUCT_TYPE => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1310 ENTRY_ADDUCT_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1311 ENTRY_DELTA => 0,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1312 ENTRY_ENTRY_INCHI => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1313 ENTRY_ENTRY_LOGP => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1314 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1315 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1316 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1317 $index_mz ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1318 $index_mz_continous ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1319 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1320 $index_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1321 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1322 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1323 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1324 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1325
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1326 =head2 METHOD write_html_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1327
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1328 ## Description : prepare and write the html output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1329 ## Input : $html_file_name, $html_object, $html_template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1330 ## Output : $html_file_name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1331 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1332
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1333 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1334 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1335 sub write_html_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1336 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1337 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1338 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1339
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1340 my $html_file = $$html_file_name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1341
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1342 if ( defined $html_file ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1343 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1344
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1345 if (-e $html_template) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1346 my $ohtml = HTML::Template->new(filename => $html_template);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1347 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1348 $ohtml->param( CONDITIONS => $search_condition ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1349 $ohtml->param( PAGES_NB => $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1350 $ohtml->param( PAGES => $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1351 print HTML $ohtml->output ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1352 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1353 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1354 croak "Can't fill any html output : No template available ($html_template)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1355 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1356
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1357 close (HTML) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1358 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1359 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1360 croak "No output file name available to write HTML file\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1361 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1362 return(\$html_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1363 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1364 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1365
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1366 =head2 METHOD set_lm_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1367
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1368 ## Description : build the hmdb_row under its ref form
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1369 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1370 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1371 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1372
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1373 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1374 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1375 sub set_lm_matrix_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1376 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1377 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1378 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1379
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1380 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1381
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1382 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1383 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1384 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1385 push @hmdb_matrix, \@headers ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1386 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1387
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1388 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1389
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1390 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1391
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1392 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1393 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1394 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1395
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1396 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1397 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1398
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1399 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1400
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1401 foreach my $entry (@{ $entries->[$index_mz] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1402
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1403 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1404 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1405 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1406 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1407
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1408 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1409
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1410 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1411
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1412 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1413 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1414 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1415
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1416 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1417 ## entry1=VAR1::VAR2::VAR3::VAR4\|entry2=VAR1::VAR2::VAR3::VAR4\|...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1418 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1419 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'\|' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1420 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1421
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1422 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1423 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1424 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1425 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1426 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1427 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1428 push (@hmdb_matrix, \@clusters) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1429 $index_mz++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1430 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1431 return(\@hmdb_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1432 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1433 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1434
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1435 =head2 METHOD set_hmdb_matrix_object_with_ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1436
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1437 ## Description : build the hmdb_row under its ref form (IDS only)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1438 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1439 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1440 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1441
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1442 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1443 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1444 sub set_hmdb_matrix_object_with_ids {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1445 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1446 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1447 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1448
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1449 # print Dumper $entries ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1450
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1451 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1452
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1453 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1454 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1455
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1456 ## redefined the header hmdb(delta::name::mz::formula::adduct::id)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1457 $header = 'hmdb(delta::name::mz::formula::adduct::id)' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1458 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1459 push @hmdb_matrix, \@headers ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1460 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1461
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1462 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1463
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1464 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1465
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1466 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1467 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1468 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1469
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1470 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1471 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1472
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1473 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1474
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1475 foreach my $entry (@{ $entries->[$index_mz] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1476
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1477 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1478 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1479 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1480 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1481
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1482 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1483
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1484 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1485 ##
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1486
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1487 my ($hmdb_name, $hmdb_id, $hmdb_formula, $hmdb_cpd_mz, $hmdb_adduct, $hmdb_delta) = (undef, undef, undef, undef, undef, undef) ;
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1488
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1489 if ($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	1490 else { $hmdb_name = 'UNKNOWN' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1491
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1492 if ($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	1493 else { $hmdb_id = 0 ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1494
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1495 if ($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	1496 else { $hmdb_formula = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1497
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1498 if ($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	1499 else { $hmdb_cpd_mz = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1500
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1501 if ($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	1502 else { $hmdb_adduct = 'N/A' ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1503
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1504 if ($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	1505 else { $hmdb_delta = 0 ; }
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	1506
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1507
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1508 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1509 ## 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	1510 my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1511
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1512 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1513 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' \| ' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1514 else { $cluster_col .= $entry ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1515
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1516 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1517 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1518 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1519 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1520 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1521 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1522 push (@hmdb_matrix, \@clusters) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1523 $index_mz++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1524 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1525 return(\@hmdb_matrix) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1526 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1527 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1528
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1529 =head2 METHOD add_lm_matrix_to_input_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1530
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1531 ## Description : build a full matrix (input + lm column)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1532 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1533 ## Output : $output_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1534 ## 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	1535
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1536 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1537 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1538 sub add_lm_matrix_to_input_matrix {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1539 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1540 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1541 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1542
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1543 my @output_matrix_object = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1544 my $index_row = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1545 my $line = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1546
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1547 foreach my $row ( @{$input_matrix_object} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1548 my @init_row = @{$row} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1549 $line++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1550
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1551 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1552 push (@output_matrix_object, \@init_row) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1553 next ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1554 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1555
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1556 if ( $lm_matrix_object->[$index_row] ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1557 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1558
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1559 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1560 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1561
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1562 push (@init_row, $lm_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1563 $index_row++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1564 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1565 push (@output_matrix_object, \@init_row) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1566 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1567 return(\@output_matrix_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1568 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1569 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1570
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1571 =head2 METHOD write_csv_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1572
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1573 ## Description : prepare and write csv output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1574 ## Input : $csv_file, $rows
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1575 ## Output : $csv_file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1576 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1577
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1578 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1579 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1580 sub write_csv_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1581 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1582 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1583 my ( $csv_file, $rows ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1584
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1585 # my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1586 my $ocsv = lib::csv::new() ;
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1587 my $csv = $ocsv->get_csv_object("\t") ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1588 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1589
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1590 return($csv_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1591 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1592 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1593
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1594 =head2 METHOD write_csv_one_mass
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1595
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1596 ## Description : print a cvs file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1597 ## Input : $masses, $ids, $results, $file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1598 ## Output : N/A
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1599 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1600
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1601 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1602 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1603 sub write_csv_one_mass {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1604 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1605 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1606 my ( $masses, $ids, $results, $file, ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1607
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1608 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	1609 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	1610
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1611 my $i = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1612
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1613 foreach my $id (@{$ids}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1614 my $mass = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1615 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1616 else { last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1617
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1618 if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1619
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1620 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1621 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1622 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1623
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1624 foreach my $entry (@{$results->[$i]}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1625 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1626 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1627 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1628 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1629 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1630 # print "\n-----------------------" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1631 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1632 # print "-------------------------$check_rebond\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1633 # print Dumper @anti_redondant ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1634 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1635
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1636 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1637
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1638 print CSV "$id\t$mass\t" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1639
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1640 ## print delta
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1641 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1642 else { print CSV "0\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1643
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1644 ## print cpd name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1645 if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1646 else { print CSV "UNKNOWN\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1647
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1648 ## print cpd mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1649 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1650 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1651
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1652 ## print cpd formula
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1653 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1654 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1655
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1656 ## print adduct
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1657 if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1658 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1659
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1660 ## print adduct mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1661 if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1662 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1663
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1664 ## print cpd id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1665 if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1666 else { print CSV "N/A\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1667 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1668 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1669 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1670 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1671 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	1672 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1673 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1674 $i++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1675 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1676 close(CSV) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1677 return() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1678 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1679 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1680
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1681 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1682
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1683
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1684 __END__
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1685
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1686 =head1 SUPPORT
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1687
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1688 You can find documentation for this module with the perldoc command.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1689
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1690 perldoc hmdb.pm
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1691
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1692 =head1 Exports
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1693
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1694 =over 4
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1695
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1696 =item :ALL is ...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1697
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1698 =back
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1699
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1700 =head1 AUTHOR
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1701
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1702 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1703
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1704 =head1 LICENSE
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1705
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1706 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	1707
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1708 =head1 VERSION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1709
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1710 version 1 : 06 / 06 / 2013
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1711
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1712 version 2 : 27 / 01 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1713
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1714 version 3 : 19 / 11 / 2014
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1715
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1716 version 4 : 28 / 01 / 2016
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1717
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1718 version 5 : 02 / 11 /2016
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1719
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1720 =cut

Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate lib/hmdb.pm @ 23:2d8a310e86ce draft