#!/usr/bin/perl
# Description: This is a template example script. I reads fasta from STDIN and produces template annotation format output
# Author: Edita Bartaseviciute
# Email: edita@cbs.dtu.dk
# Version: 1.02 ws0
# Date: 2008-09-15
# usage: perl chemprot.pl < example.fsa

# include standard XML::Compile helper functions (used to initiate WSDL proxys)
use Data::Dumper;
use strict;
require "xml-compile.pl";

# create proxy to genome atlas
my $chemprot = WSDL2proxy ( 'http://www.cbs.dtu.dk/ws/ChemProt/ChemProt_1_02_ws0.wsdl' );

# append schema definitions
$chemprot = appendSchemas ( $chemprot , 
	"http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd" ,
	"http://www.cbs.dtu.dk/ws/ChemProt/ws_chemprot_1_02_ws0.xsd"
);

my %ops = addOperations ( $chemprot ) ;

my @fasta;
my $entry = -1;

while (<>) {
	if (/^>(.*)/) {
		my ($id , $comment) = split (" ",$1);
		$entry++;
		$fasta[$entry]->{id} = $id;
		$fasta[$entry]->{comment} = $comment if defined $comment;
	} elsif (/^([A-Za-z]+)/) {
		$fasta[$entry]->{seq} .= $1;
	}
}
my @sequence;
for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i ++ ) {
	push @sequence , { id => $fasta[$i]->{id} , comment => $fasta[$i]->{comment} , seq => $fasta[$i]->{seq} };
}

my $response = $ops{runService}->(
	 parameters => {
	  parameters => {
#	   organism => 'euk' ,
#	   method => 'nn+hmm' ,
#	   thnn => '0.43' ,
	   sequencedata => {sequence => [@sequence]} } });

my $jobid;

if ( ! defined ( $response->{parameters}->{queueentry}) ) {
	die "error obtaining jobid\n";
} else {
	$jobid = $response->{parameters}->{queueentry}->{jobid};
	print STDERR "# waiting for job $jobid";
	my $status = "UNKNOWN";;
	while ( $status =~ /ACTIVE|RUNNING|QUEUED|WAITING|PENDING|UNKNOWN/ ) {
		my $response = $ops{pollQueue}->( job => { job  => { jobid => $jobid }   }) ;
		$status = $response->{queueentry}->{queueentry}->{status};
		print STDERR  ".";
	}
	die "\nunexpected job status '$status'\n" unless $status eq "FINISHED";
	print STDERR "\n# job has finished\n";
}

$response = $ops{fetchResult}->(job => { jobid => $jobid });
print "method           : ".$response->{parameters}->{anndata}->{annsource}->{method}."\n";
print "version          : ".$response->{parameters}->{anndata}->{annsource}->{version}."\n";
foreach my $ann (@{$response->{parameters}->{anndata}->{ann}}) {
	print " sequence id      : $ann->{sequence}->{id}\n";
	print " sequence comment : $ann->{sequence}->{comment}\n";
	print " sequence         : $ann->{sequence}->{seq}\n";
	foreach my $annrecord (@{$ann->{annrecords}->{annrecord}}) {
			print join ( "\t", ( 
					$annrecord->{feature},
					$annrecord->{range}->{begin}->numify,
					$annrecord->{range}->{end}->numify,
					$annrecord->{score}[0]->{key}.':'.$annrecord->{score}[0]->{value},
				))."\n";
		}}