view lib/golm_ws_api.pm @ 0:e3d43b8c987b draft

Init repository with last tool-bank-golm-lib_search master version

package lib::golm_ws_api ;

use strict;
use warnings ;
use Exporter ;
use Carp ;

use Data::Dumper ;
#use SOAP::Lite +trace => [qw (debug)];
use SOAP::Lite ;
use JSON ;

use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);

our $VERSION = "1.0";
our @ISA = qw(Exporter);
our @EXPORT = qw( connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results);
our %EXPORT_TAGS = ( ALL => [qw( connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results)] );

=head1 NAME

My::Module - An example module

=head1 SYNOPSIS

    use My::Module;
    my $object = My::Module->new();
    print $object->as_string;

=head1 DESCRIPTION

This module does not really exist, it
was made for the sole purpose of
demonstrating how POD works.

=head1 METHODS

Methods are :

=head2 METHOD new

	## Description : new
	## Input : $self
	## Ouput : bless $self ;
	## Usage : new() ;

=cut

sub new {
    ## Variables
    my $self={};
    bless($self) ;
    return $self ;
}
### END of SUB
     
=head2 METHOD connectWSlibrarySearchGolm

	## Description : create a soap object throught the webservice LibrarySearch of Golm.
	## Input : $ws_url, $ws_proxy
	## Ouput : $soap ;
	## Usage : my $soap = connectWSlibrarySearchGolm($ws_url, $ws_proxy) ;

=cut

sub connectWSlibrarySearchGolm() {
	## Retrieve Values
    my $self = shift ;
    my ($ws_url, $ws_proxy) = @_ ;
    
	my $osoap = SOAP::Lite
		-> soapversion('1.2')
		-> envprefix('soap12')
		-> readable(1)
		-> uri( $ws_url )
		-> proxy( $ws_proxy."/" )
		-> on_fault(sub { my($soap, $res) = @_; 
         eval { die ref $res ? $res->faultstring : $soap->transport->status, "\n"};
         return ref $res ? $res : new SOAP::SOM ;
         });
	
	return ($osoap);
}
### END of SUB
     
     
     
     
     
=head2 METHOD test_query_golm

	## Description : send a test request (default given on ws website) to golm database.
	## Input : $ws_url, $ws_proxy
	## Ouput : $soap ;
	## Usage : my $soap = test_query_golm($ws_url, $ws_proxy) ;

=cut

sub test_query_golm() {
	## Retrieve Values
    my $self = shift ;
    my ($ws_url, $ws_proxy) = @_ ;
    
	my $soap = SOAP::Lite
              -> uri($ws_url)
              -> on_action( sub { join '/', $ws_proxy, $_[1] } )
              -> proxy($ws_proxy, timeout => 500);
               
           # Setting Content-Type myself
           my $http_request = $soap
              ->{'_transport'}
              ->{'_proxy'}
              ->{'_http_request'};
           $http_request->content_type("text/xml; charset=utf-8");
           
            my $method = SOAP::Data->name('LibrarySearch')
                ->attr({xmlns => $ws_proxy."/"});
           
            my @params = (
                           SOAP::Data->name('ri' => 1898),
                           SOAP::Data->name('riWindow' => 5),
                           SOAP::Data->name('AlkaneRetentionIndexGcColumnComposition' => 'VAR5'),
                           SOAP::Data->name('spectrum' => "70 3 71 3 72 16 73 999 74 87 75 78 76 4 77 5 81 1 82 6 83 13 84 4 85 3 86 4 87 5 88 4 89 52 90 4 91 2 97 2 98 1 99 4 100 12 101 16 102 9 103 116 104 11 105 26 106 2 107 1 111 1 112 1 113 4 114 11 115 7 116 5 117 93 118 9 119 8 126 1 127 3 128 3 129 101 130 19 131 25 132 4 133 60 134 8 135 4 140 1 141 1 142 4 143 13 144 2 145 6 146 1 147 276 148 44 149 27 150 3 151 1 156 1 157 70 158 12 159 5 160 148 161 26 162 7 163 8 164 1 168 1 169 2 170 1 172 3 173 4 174 1 175 4 177 4 186 2 187 1 189 28 190 7 191 13 192 2 193 1 201 5 202 1 203 3 204 23 205 162 206 31 207 16 208 2 210 2 214 1 215 2 216 8 217 88 218 18 219 8 220 1 221 6 222 1 229 23 230 6 231 11 232 3 233 4 234 3 235 1 243 1 244 2 245 1 246 2 247 1 256 1 262 3 263 1 269 2 270 1 274 4 275 1 277 4 278 1 291 7 292 2 293 1 300 1 305 4 306 1 307 4 308 1 318 1 319 122 320 37 321 17 322 3 323 1 343 1 364 2 365 1" ) );
			
			my $som = $soap->call($method => @params);
			die $som->faultstring if ($som->fault);
			
			## Get the hits + status of the query
			my $results = $som->result->{Results} ;
			my $status = $som->result->{Status} ;

			if ($status eq 'success' && $results ne '') {
				print "\n\n\nThe test request succeeded - Golm Service available.\n\n\n" ;
				return 1 ;
			}
			else { croak "\n\n\nSomething went wrong with the test request. Status delivered by Golm = ".$status."\n\n" ; }
}
### END of SUB
     
     

=head2 METHOD LibrarySearch

	## Description : Matches a single user submitted GC-EI mass spectrum against the Golm Metabolome Database (GMD). 
	## 				 A limited amount of hits can be kept according to the maxHits value and after them being filtered by $filter value
	## Input : $osoap, $ri, $riWindow, $gcColumn, $spectrum, $maxHits
	## Ouput : \@limited_hits, \@json_res
	## Usage : ($limited_hits,$json_res) = LibrarySearch($osoap, $ri, $riWindow, $gcColumn, $spectrum, $maxHits) ;

=cut

sub LibrarySearch() {
	## Retrieve Values
	my $self = shift ;
	my ($ri, $riWindow, $gcColumn, $spectrum, $maxHits,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,$DotproductDistanceThreshold,
		$HammingDistanceThreshold,$EuclideanDistanceThreshold, $ws_url, $ws_proxy, $default_ri, $default_ri_window, $default_gc_column) = @_ ;

	#init in case :
	$ri = $default_ri if ( !defined $ri ) ;
	$riWindow = $default_ri_window if ( !defined $riWindow ) ;
	$gcColumn = $default_gc_column if ( !defined $gcColumn ) ;
	
	
	my $result ;
	my @filtered_limited_res = () ;
	my @json_res ;
	
	if ( defined $spectrum ){
		    	
    	if ( $spectrum ne '' ) {
    		
		   my $soap = SOAP::Lite
              -> uri($ws_url)
              -> on_action( sub { join '/', $ws_proxy, $_[1] } )
              -> proxy($ws_proxy);
               
           # Setting Content-Type myself
           my $http_request = $soap
              ->{'_transport'}
              ->{'_proxy'}
              ->{'_http_request'};
           $http_request->content_type("text/xml; charset=utf-8");
           
            my $method = SOAP::Data->name('LibrarySearch')
                ->attr({xmlns => $ws_proxy."/"});
           
            my @params = (
                           SOAP::Data->name('ri' => $ri),
                           SOAP::Data->name('riWindow' => $riWindow),
                           SOAP::Data->name('AlkaneRetentionIndexGcColumnComposition' => $gcColumn),
                           SOAP::Data->name('spectrum' => $spectrum) ) ;
			
			my $som = $soap->call($method => @params);
			die $som->faultstring if ($som->fault);
			
			## Get the hits + status of the query
			my $results = $som->result->{Results} ;
			my $status = $som->result->{Status} ;
            
            ## Limitate number of hits returned according to user's $maxHit
            ## and filter hits on specific values with thresholds
            my @results = @$results ;
            
            ### Return all hits
            my $oapi = lib::golm_ws_api->new() ;
            if ($maxHits == 100 && $status eq 'success') {
            	
            	my $filtered_res = $oapi->filter_scores_golm_results(\@results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
																		$DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
            	
            	if(!@$filtered_res){ push (@$filtered_res , "no results") ; }
            	
            	return ($filtered_res) ;
            }
            elsif ($maxHits < 100 && $maxHits > 0 && $status eq 'success'){
            	
            	my $filtered_res_before_hits_limited = $oapi->filter_scores_golm_results(\@results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
																		$DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
            	if (@$filtered_res_before_hits_limited) {
            		
	            	for (my $i=0 ; $i<$maxHits ; $i++) {
	            		
		            	push (@filtered_limited_res , @$filtered_res_before_hits_limited[$i]) ;
	            	}
            	}
            	else {
            		
	            	if(!@$filtered_res_before_hits_limited){ push (@filtered_limited_res , "no results") ; }
            	}
            	return (\@filtered_limited_res) ;
            }
            else { carp "No match returned from Golm for the query.\n" }
        }
    	else { carp "The spectrum for query is empty, Golm soap will stop.\n" ; }
    }
    else { carp "The spectrum for query is undef, Golm soap will stop.\n" ; }
	
	return \@filtered_limited_res ;
}
### END of SUB




=head2 METHOD filter_scores_golm_results
	## Description : filter golm's hits by distance scores 
	## Input : $results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
	##		   $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold
	## Ouput : \@filtered_res ;
	## Usage : my ($filtered_res) = filter_scores_golm_results($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
	##															$DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;

=cut

sub filter_scores_golm_results() {
	## Retrieve Values
	my $self = shift ;
	my ($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
		$DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) = @_ ;
		
	my @results = @$results ;
	my @filtered_res = () ;
	
	foreach my $res (@results){

			if ($res->{'JaccardDistance'} <= $JaccardDistanceThreshold && $res->{'s12GowerLegendreDistance'} <= $s12GowerLegendreDistanceThreshold
				&& $res->{'DotproductDistance' } <= $DotproductDistanceThreshold && $res->{'HammingDistance'} <= $HammingDistanceThreshold && 
				$res->{'EuclideanDistance' } <= $EuclideanDistanceThreshold) {
					
				push (@filtered_res , $res) ;
			}
	}
	
	my $oapi = lib::golm_ws_api->new() ;
	my $sorted_analytes = $oapi->filter_replica_results(\@filtered_res) ;
	
	return $sorted_analytes ;
}



=head2 METHOD _filter_replica_results
     ## Description : remove replicated hits, keep the ones with the lowest dot product distance
     ## Input : $results
     ## Ouput : \@clean_res ;
     ## Usage : my ($clean_res) = filter_replica_results($results) ;

=cut

sub filter_replica_results() {
     ## Retrieve Values
     my $self = shift ;
     my ($results) = @_ ;
	 my %seen ;
	 my @sortAnalytes = grep { !$seen{$_->{'analyteName'}}++ } sort { $a->{'DotproductDistance'} <=> $b->{'DotproductDistance'} } @$results ;

     return \@sortAnalytes ;
}




	
1 ;


__END__

=head1 SUPPORT

You can find documentation for this module with the perldoc command.

 perldoc golm_ws_api.pm

=head1 Exports

=over 4

=item :ALL is connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results

=back

=head1 AUTHOR

Franck Giacomoni E<lt>[e-mail]<gt>
Gabriel Cretin E<lt>[e-mail]<gt>

=head1 LICENSE

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

=head1 VERSION

version 1 : 03 / 06 / 2016

version 2 : 24 / 06 / 2016

=cut