diff lib/threader.pm @ 0:023c380900ef draft default tip

Init repository with last massbank_ws_searchspectrum master version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/threader.pm	Wed Apr 19 11:31:58 2017 -0400
@@ -0,0 +1,264 @@
+package lib::threader ;
+
+use strict;
+use warnings ;
+use Exporter ;
+use Carp ;
+use threads;
+use threads::shared;
+use Thread::Queue;
+use diagnostics ;
+use Data::Dumper ;
+use Carp qw (cluck croak carp) ;
+use LWP::UserAgent;
+use LWP::Simple ; ## Lib de protocole HTTP de download
+use SOAP::Lite + trace => qw(fault); ## SOAP for web service version 0.67
+import SOAP::Data qw(name);
+
+use Data::Dumper ;
+
+use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
+
+our $VERSION = "1.0";
+our @ISA = qw(Exporter);
+our @EXPORT = qw(threading_getRecordInfo);
+our %EXPORT_TAGS = ( ALL => [qw(threading_getRecordInfo )] );
+
+=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 searchSpectrumWorker
+
+	## Description : work with searchSpectrum method in threading mode
+	## Input : $Qworks
+	## Output : $results
+	## Usage : my ( $results ) = searchSpectrumWorker( $Qworks ) ;
+	
+=cut
+## START of SUB
+sub searchSpectrumWorker {
+	my $self = shift;
+	my ($Qworks, $server, $ion_mode, $instruments, $max, $unit, $tol, $cutoff) = @_ ;
+	my @results = () ;
+	my @fake = () ;
+
+	my $omassbank = lib::massbank_api->new() ;
+	my $soap = $omassbank->selectMassBank($server) ;
+	
+	while(my $pcgroup = $Qworks->dequeue) {
+#		print Dumper $pcgroup ;
+	    my $oquery= lib::massbank_api->new() ;
+		my ($result, $num) = eval{$oquery->searchSpectrum($soap, $pcgroup->{'id'}, $pcgroup->{'mzmed'}, $pcgroup->{'into'}, $ion_mode, $instruments, $max, $unit, $tol, $cutoff) ; } or die;
+#		print "The query send to massbank return $num entries...\n" ;
+#		print Dumper $result ;
+
+		if (!defined $num) { $num = 0  ; }
+		if ($num >= 0 ) {
+			push @results, $result ;
+		}
+		else {
+			push @fake, $pcgroup ;
+		}
+    }
+	return (@results) ;
+}
+## END of SUB
+
+   
+=head2 METHOD threading_getRecordInfo
+
+	## Description : prepare parallel threads - DEPRECATED
+	## Input : $soap, $list
+	## Output : $results
+	## Usage : my ( $results ) = threading_getRecordInfo( $soap, $list ) ;
+	
+=cut
+## START of SUB
+sub threading_getRecordInfo {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $osoap, $list ) = @_ ;
+    
+    my @results = () ;
+    my $i = 0 ; # position in the ids list
+    
+    if ( ( defined $list ) ) {
+    	
+    	my $oquery = lib::massbank_api->new() ;
+    	
+    	for (my $i = 0; $i < (scalar @{$list}); $i++ ) {
+    		my $thr = threads->create( sub { $oquery->getRecordInfo($osoap, $list->[$i]) } ) ;
+    		push ( @results, $thr->join )  if $list->[$i] ;
+    	}
+    }
+    else {
+    	warn "Your input list of ids is undefined\n" ;
+    }
+    return(\@results) ;
+}
+## END of SUB
+
+
+=head2 METHOD threading_searchSpectrum
+
+	## Description : prepare parallel threads - DEPRECATED
+	## Input : $soap, 
+	## Output : $results
+	## Usage : my ( $results ) = threading_searchSpectrum( $soap,  ) ;
+	
+=cut
+## START of SUB
+sub threading_searchSpectrum {
+	
+	## http://www.perlmonks.org/?node_id=735923
+	## http://www.nntp.perl.org/group/perl.ithreads/2003/05/msg696.html
+	## http://stackoverflow.com/questions/15222480/web-service-using-perl-wsdl-and-multi-threading-does-not-working
+	## Retrieve Values
+    my $self = shift ;
+    my ( $osoap, $pcgroup_list, $pcgroups, $ion_mode, $instruments, $max, $unit, $tol, $cutoff ) = @_ ;
+    
+    my @results = () ;
+    my $n = 6 ; # position in the ids list
+    
+    if ( ( defined $pcgroups ) ) {
+    	
+    	print Dumper $pcgroups ;
+    	
+    	my $oquery = lib::massbank_api->new() ;
+    	
+    	foreach my $pc (@{$pcgroup_list}) {
+    		
+    		print "\t---> Create a thread for pcgroup n-$pc\n" ;
+    		
+    		my $thr = threads->create(
+    			sub { 
+    					$oquery->searchSpectrum($osoap, $pcgroups->{$pc}{'mzmed'}, $pcgroups->{$pc}{'into'}, $ion_mode, $instruments, $max, $unit, $tol, $cutoff) ;
+    			} 
+    		) ;
+    		push ( @results, $thr->join ) ;
+    	} ## end foreach
+    }
+    else {
+    	warn "Your input list of ids is undefined\n" ;
+    }
+    return(\@results) ;
+}
+## END of SUB
+
+
+=head2 METHOD thread_and_queue_searchSpectrum
+
+	## Description : prepare parallel and queuing threads - DEPRECATED
+	## Input : $soap, 
+	## Output : $results
+	## Usage : my ( $results ) = thread_and_queue_searchSpectrum( $soap,  ) ;
+	
+=cut
+## START of SUB
+sub thread_and_queue_searchSpectrum {
+#    my $self = shift;
+#    my ( ) = @_;
+#    
+#    our $THREADS = 10;
+#	my $Qwork = new Thread::Queue;
+#	my $Qresults = new Thread::Queue;
+#	
+#	## Create the pool of workers
+#	my @pool = map{
+#	    threads->create( \&worker, $Qwork, $Qresults )
+#	} 1 .. $THREADS;
+#	
+#	## Get the work items (from somewhere)
+#	## and queue them up for the workers
+#	while( my $workItem = getWorkItems() ) {
+#	    $Qwork->enqueue( $workItem );
+#	}
+#	
+#	## Tell the workers there are no more work items
+#	$Qwork->enqueue( (undef) x $THREADS );
+#	
+#	## Process the results as they become available
+#	## until all the workers say they are finished.
+#	for ( 1 .. $THREADS ) {
+#	    while( my $result = $Qresults->dequeue ) {
+#	
+#	        ## Do something with the result ##
+#	        print $result;
+#	    }
+#	}
+#	
+#	## Clean up the threads
+#	$_->join for @pool;
+}
+## END of SUB
+
+
+
+1 ;
+
+
+__END__
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+ perldoc XXX.pm
+
+=head1 Exports
+
+=over 4
+
+=item :ALL is ...
+
+=back
+
+=head1 AUTHOR
+
+Franck Giacomoni 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 : xx / xx / 201x
+
+version 2 : ??
+
+=cut
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