SIDDbase test

#!/usr/bin/perl
# Description: Standalone test script - all prerequisites embedded
# Author: Peter Fischer Hallin
# Email: pfh@cbs.dtu.dk
# Version: 1.0a
# Date: 2009-05-04

use Data::Dumper;
use strict;
use XML::Compile;
use XML::Compile::WSDL11;
use XML::Compile::Transport::SOAPHTTP;
use MIME::Base64;
use URI::WithBase;

my $proxy = WSDLclient ( 'http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0a_ws0.wsdl' );

# input parameters for retrieving the sequence information
print STDERR "submitting getSIDD request...\n";
my $response = $proxy->{getSIDD}->( 
 parameters => { 
  parameters => {
   accession => 'AL111168' ,
   energetics => 'c' , 
   sigma => '-0.045' , 
   weight => '10' , 
   from => '100' , 
   to => '120' , 
   Gformat => '%0.2f' , 
   Pformat => '%0.10f' , 
   format => 'element' , 
  }
 }
);

die "unexpected response\n" unless scalar ( @{$response->{parameters}->{output}->{element}->{pos}}) > 0;

printf STDERR "getSIDD parsed (%d entries obtained)\n", scalar ( @{$response->{parameters}->{output}->{element}->{pos}});

# read fasta from stdin
print STDERR "reading fasta from stdin...\n";
my @fasta = read_fasta();

my $ENERGETICS = "c";
my $GEOMETRY = "c";
my $SIGMA = "-0.045";
my $WEIGHT = '10';

for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i++ ) {
	runSIDD (
	 $proxy,
	 $fasta[$i]->{id},
	 $fasta[$i]->{comment},
	 $fasta[$i]->{seq},
	 $ENERGETICS,
	 $GEOMETRY,
	 $SIGMA,
	 $WEIGHT
	);
}

printf "runSIDD parsed (%d entries obtained)\n", scalar ( @{$response->{parameters}->{output}->{element}->{pos}});
exit 0;

sub runSIDD {
	my ($proxy,$id,$comment,$seq,$energetics,$geometry,$sigma,$weight,$format) = @_;
	print STDERR "submitting runService request (id $id)...\n";
	my $response = $proxy->{runService}->(
	  parameters => {
	   parameters => {
	    sequencedata => { 
	     sequence => [ {
	      id => $id , 
	      comment => $comment , 
	      seq => $seq ,
	     } ]
	    } ,
	    energetics => $energetics ,
	    geometry => $geometry ,
	    sigma => $sigma ,
	    weight => $weight ,
	    format => 'element' ,
	   }
	  }
	 );
	my ($jobid,$status,$expires);
	die "error obtaining jobid\n" unless defined ( $response->{parameters}->{queueentry});
	$jobid = $response->{parameters}->{queueentry}->{jobid};
	wait_job($proxy->{pollQueue},$jobid);
	$response = $proxy->{fetchResult}->( job => { jobid => $jobid   }) ;
	die "unexpected response\n" unless scalar ( @{$response->{parameters}->{output}->{element}->{pos}}) > 0;
	printf STDERR "obtained r...\n";
	printf STDERR "fetchResult parsed (%d entries obtained)\n", scalar ( @{$response->{parameters}->{output}->{element}->{pos}});
}

sub read_fasta {
	my $filename = $_[0];
	my @LINES;
	if ( defined ( $filename ) ) {
		open FASTA, $filename or die("Unable to open FASTA.\n");
		while (<FASTA>) {
			push @LINES , $_;
		}
		close FASTA;
	} else {
		while (<DATA>) {
			push @LINES , $_;
		}
	}
	my @fasta;
	my $seqentry = -1;
	foreach my $line ( @LINES ) {
		chomp $line;
		if ($line=~ m/^>(.*)/) {
			$seqentry++;
			my $id = $1 if $line =~ /^>(\S+)/;
			my $comment = $1 if $line =~ /^>\S+\s+(.*)/;
			$fasta[$seqentry]{comment} = $comment if defined $comment;
			$fasta[$seqentry]{seqentry} = $seqentry;
			$fasta[$seqentry]{id} = $id;
		} elsif ($line =~ m/^([A-Za-z\-]+)/) {
				$fasta[$seqentry]{seq} .= uc ( $1 );
		}
	}
	return @fasta;
}

sub wait_job {
	my ($op_handle,$jobid) = @_;
	my $sleep = 0;
	my $status = "UNKNOWN";
	my $response;
	while ( $status !~ /FINISHED|FAILED/ ) {
		$response = $op_handle->( job => { job  => { jobid => $jobid }   }) ;
		my $new_status = $response->{queueentry}->{queueentry}->{status};
		if ( $new_status ne $status and $new_status ne "") {
			print STDERR "# job $jobid $new_status ($response->{queueentry}->{queueentry}->{datetime})\n";
			$status = $new_status;
		}
		$sleep = 5 if $status eq "ACTIVE";
		sleep $sleep;
	}
	die "# ERROR: job $jobid FAILED\n" if $status ne "FINISHED";
}

# with time, this is to replace the above functions!

sub WSDLclient {
	# by hhs 2008
	my ($wsdlurl, @ops)=@_;
	my %imports=();	
	my $importcnt;
	my %ops;
	my $wsdl = XML::LibXML->new->parse_file($wsdlurl);
	my $proxy = XML::Compile::WSDL11->new($wsdl);
		while (1) {
		foreach my $ns (keys %{$proxy->{schemas}->{namespaces} }) {
			foreach my $uri (keys %{$proxy->{schemas}->{namespaces}->{$ns}}) {
				foreach my $e (@{$proxy->{schemas}->{namespaces}->{$ns}->{$uri}}) {
					my $base = $wsdlurl;
					$base = $e->{filename} if defined $e->{filename};
					foreach my $ns2 (keys %{$e->{import}} ) {
						foreach my $fn ( @{$e->{import}->{$ns2}} ) {
							$uri = URI::WithBase->new($fn, $base);
							$imports{$uri->abs}=0 unless (defined $imports{$uri->abs});
						}
					}
				}
			}
		}
		$importcnt=0;
		foreach my $url (keys %imports) {
			next if $imports{$url} == 1; # added by pfh
			my $f = XML::LibXML->new->parse_file($url);
			$proxy->schemas->importDefinitions ($f);			
			$importcnt++;
			$imports{$url}=1;
		}
		last unless($importcnt);
	}
	my %inc;
	if ( $#ops >= 0) {
		foreach (@ops) {
			$inc{$_} = 1;
		}
	}
	foreach my $op ($proxy->operations) {
		next if $#ops >= 0 and ! defined $inc{$op->{operation}};
		$ops{$op->{operation}} = $proxy->compileClient($op->{operation});
	}
	return \%ops;	
}

__DATA__
>FM180570 
GATATATTTATTTCCAAAATGCTACAGATACATCATCATGAAACGGATCACCGCAAACAG
GTTACTCGCCTGGGGATTCCCTTTCGACCCGAGCATCCGTATGAGACTCATGCTCGATTA
TTATTATTATAGAAGCCCCCATGAATAAATCGCTCATCATTTTCGGCATCGTCAACATAA
CCTCGGACAGTTTCTCCGATGGAGGCCGGTATCTGGCGCCAGACGCAGCCATTGCGCAGG
CGCGTAAGCTGATGGCCGAGGGGGCAGATGTGATCGACCTCGGTCCGGCATCCAGCAATC
CCGACGCCGCGCCTGTTTCGTCCGACACAGAAATCGCGCGTATCGCGCCGGTGCTGGACG
CGCTCAAGGCAGATGGCATTCCCGTCTCGCTCGACAGTTATCAACCCGCGACGCAAGCCT
ATGCCTTGTCGCGTGGTGTGGCCTATCTCAATGATATTCGCGGTTTTCCAGACGCTGCGT
TCTATCCGCAATTGGCGAAATCATCTGCCAAACTCGTCGTTATGCATTCGGTGCAAGACG
GGCAGGCAGATCGGCGCGAGGCACCCGCTGGCGACATCATGGATCACATTGCGGCGTTCT
TTGACGCGCGCATCGCGGCGCTGACGGGTGCCGGTATCAAACGCAACCGCCTTGTCCTTG
ATCCCGGCATGGGGTTTTTTCTGGGGGCTGCTCCCGAAACCTCGCTCTCGGTGCTGGCGC
GGTTCGATGAATTGCGGCTGCGCTTCGATTTGCCGGTGCTTCTGTCTGTTTCGCGCAAAT
CCTTTCTGCGCGCGCTCACAGGCCGTGGTCCGGGGGATGTCGGGGCCGCGACACTCGCTG
CAGAGCTTGCCGCCGCCGCAGGTGGAGCTGACTTCATCCGCACACACGAGCCGCGCCCCT
TGCGCGACGGGCTGGCGGTATTGGCGGCGCTGAAAGAAACCGCAAGAATTCGTTAACTGC
ACATTCGGGATATTTCTCTATATTCGCGCTTCATCAGAAAACTGAAGGAACCTCCATTGA
ATCGAACTAATATTTTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAG
AATCTGGTGATTTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTG
CTTCCCGCCGCGGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAG
GTGTGGCTTGCCCCGAGGTCATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGA
TAACGGCAATTCCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGT
GGCCGTCAATGGGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGT
TTGAGCGCAGGCTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCG
TCAATCCCGACTTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTC
GTGTCGAACGAGAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCC
ATGGTGATCCCTGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTC
TGATCGACCTTGGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTG
CTAACGCCGAAGAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTAT
TCAATGTATTGGGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGG
ACCCTCTGACTTGGGGTTGATGTTCATGCCGCCTGTTTTTCCTGCTCATTGGCACGTTTC
GCAACCTGTTCTCATTGCGGACACCTTTTCCAGCCTCGTTTGGAAAGTTTCATTGCCAGA
CGGGACTCCTGCAATCGTCAAGGGATTGAAACCTATAGAAGACATTGCTGATGAACTGCG
CGGGGCCGACTATCTGGTATGGCGCAATGGGAGGGGAGCAGTCCGGTTGCTCGGTCGTGA
GAACAATCTGATGTTGCTCGAATATGCCGGGGAGCGAATGCTCTCTCACATCGTTGCCGA
GCACGGCGACTACCAGGCGACCGAAATTGCAGCGGAACTAATGGCGAAGCTGTATGCCGC
ATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCGATCCGGGATCGCTTTGCAGCTTTGTT
TCAGCGGGCGCGCGATGATCAAAACGCAGGTTGTCAAACTGACTACGTCCACGCGGCGAT
TATAGCCGATCAAATGATGAGCAATGCCTCGGAACTGCGTGGGCTACATGGCGATCTGCA
TCATGAAAACATCATGTTCTCCAGTCGCGGCTGGCTGGTGATAGATCCCGTCGGTCTGGT
CGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTCTACGATCCGGCTGACAGAGACGACCT
TTGTCTCGATCCTAGACGCATTGCACAGATGGCGGACGCATTCTCTCGTGCGCTGGACGT
CGATCCGCGTCGCCTGCTCGACCAGGCGTACGCTTATGGGTGCCTTTCCGCAGCTTGGAA
CGCGGATGGAGAAGAGGAGCAACGCGATCTAGCTATCGCGGCCGCGATCAAGCAGGTGCG
ACAGACGTCATACTAGATATCAAGCGACTTCTCCTATCCCCTGGGAACACATCAATCTCA
CCGGAGAATATCGCTGGCCAAAGCCTTAGCGTAGGATTCCGCCCCTTCCCGCAAACGACC
CCAAACAGGAAACGCAGCTGAAACGGGAAGCTCAACACCCACTGACGCATGGGTTGTTCA
GGCAGTACTTCATCAACCAGCAAGGCGGCACTTTCGGCCATCCGCCGCGCCCCACAGCTC
GGGCAGAAACCGCGACGCTTACAGCTGAAAGCGACCAGGTGCTCGGCGTGGCAAGACTCG
CAGCGAACCCGTAGAAAGCCATGCTCCAGCCGCCCGCATTGGAGAAATTCTTCAAATTCC
CGTTGCACATAGCCCGGCAATTCCTTTCCCTGCTCTGCCATAAGCGCAGCGAATGCCGGG
TAATACTCGTCAACGATCTGATAGAGAAGGGTTTGCTCGGGTCGGTGGCTCTGGTAACGA
CCAGTATCCCGATCCCGGCTGGCCGTCCTGGCCGCCACATGAGGCATGTTCCGCGTCCTT
GCAATACTGTGTTTACATACAGTCTATCGCTTAGCGGAAAGTTCTTTTACCCTCAGCCGA
AATGCCTGCCGTTGCTAGACATTGCCAGCCAGTGCCCGTCACTCCCACTCTTACATTGTT
CGCAGTATCTAGGTACATGTTATTGCGTGCACCTTCATGATGTATAATGTTATTAATGAC
AGCAGAAAGATCGACAGAATTAATATTCTTCGTACCTGGGACAGTTATCGGGTGTCGGCC
AGTGATGAGACCAAAGGATGCAGTATAAGATGAACCACTACTATTATCATGGCCACCATT
ACCACCACCGTTAAAACTACCTCCCGAACTTCCAGAGCCGCTATGACCATCATTGTAGGG
GTCATTTGGTCCCATGTGACCAAAACCACCGACAGTACCGCTATTTAACTCTGTACTCAT
AAAATTATCCTCTTTGACTTTTAAAAACAGCAAAAACTGTATTTATAACAATGTGTTTAT
ATACAGTATTCGAAATACTACGCCCGTCAAAACCACACCGTCAACAGGTTTTTTGTGTAT
TTTTCACGCCTCACGGGCAGCCTCAGACCTTTTGTGTTAAAACAGTAATATGTTCTGCTG
TTACAATACGGTACACACAGGAGACACTGTCACTTTTATGGCATGGCACACAGTTCAAGA
GACACTGAAATTAACAGGAAAGTCGCGCTCGCAATTATATCGTGACATGGCTAAAGGCCT
TGTCAGCTATCGCACAGGAAAAAATGATCGCCGGGAGTTCGAGACCAGTGAACTGATTCG
GGCCTATGGCGAGCTGCGCACTTCTGAGACACCAAAAAGGCACAAGGAGGGACACTCCAA
ATCTGTCGTTAGCCAGGCGGAAAATGCTCAGCTAGACGTCATTCAGCAGAAACTGGACGC
TCTGCAGCAGACTGTTACCCTAATGCTTGAAGACAAGATGGCGCGGGAAGCAGAAAACCG
CCTGCGAAATGAGGAGAGGGAACAACTACAGGCCGAAATTAGCCGTCTGGCTGACGCGCT
GGCACAGGAAAAAAAGCGGGGATTCTGGTCGCGGCTGTTTCGCTCCGGTTCAGAGTAACA
GTGCAGGTGACTCTGATTTACCATAACATCTGTTATCAGCACCGCCTGAGAGGCCCTCAG
GGCGTTTCTGACGGGAAACCGGTAAAACAGGCAACAAACCACCCGAAAACCCGCCAGAAA
CGCGCAGGCTCTGTTTTTACGGCATGCATGAGTATGCGCACAAGTGCATAGCGCGGAAAT
TCACACCATTCAGCCGGGGTAAGTCCTGTTTCCGGCGTTCTTCCCATCCGAAAACGGTGA
ACGGGGACGCAATTTATTGCGTGGCCGTGAAGCGTTGCCGGCGCAGCCGGAAAACCCGCT
GTCAGCACGTTCAGGAAGGGGGTGATGTACAAATGGCACAGAGGATGAAAGTGACGTATG
AGCTGAAGGAGCGATGTAATTCTGTAGTCAGGAAGAATAACCCGTTCATGCAGGCATGAA
CGATACAGTGAGGAACGCTTTTTTTGTCACGATCTCCCCTTAACCTGCGTAAATCACCCG
CCATGGTTGATTATTTTTCAACCTCAAAATGGTCATACACCTAACGCAGCCGCGATTTTC
ATCGCAACTGCATGAATTAAAAGAAAAAAAAGGAATATTTCGTTTTCACGAGTAATACCC
GGGTATTAAAAATCCACTGTAATTACATGAAAATAAAGAAATAAAAGGTAATACCGGAGT
ATTACCACGTACGCGGGCAAGCGAAAAAGCTATAACGCTTCCCGGCCGACAGGCGACCCA
AAATCCACAGGGGCATGCAGGTTCTCTTCAGTAACCTGCGCCATTAAATCAAAAAGGTCA
TATTCGCCGGGAAGCTGCGTATCAGTCGAATCCAGTTGTTCATCATATTCAGATGGCATG
GGGTGATATCCAGTAGCTGAGAGGTTGTTAGCGGGTTTCGGGGCGCAGCCCTGAACCAGT
CATGTAGCGCTAGCGGAGTGTATACTGGCTTACTATGTTGCCACGATTGCGAAAATCAGT
GAAGTGCTTCATGTGGCAGGAGAAAAAAGGCAGCACCGGCGCGTCAGCAGAATATGCGAT
ACAGGAGATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGGCTGCGGC
GAGCGGTACCGGCTTACGGACGGGGACGGAAATTTCCTGGAAGATACCAGGAAGACACTT
AGCAAAGAAGAGATAAGGCCACGGCGAAGCCGTTTTTCCATAGGCTCCGCCCCCCTGACA
AGCATCGCAAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACTATAAAGAT
CCCAGGCGTTTCCCCCTGGTAGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCGGTTTA
CCGGTGTCATTCCGCTGTTATGGCCGCGGTTTCTCATTCCACGCCTGACACTCAGTTCCG
TGAAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCCGTTCAGTCCGACCGCT
GCGCCTTGTCCGGTAACTATCAACTTGAGTCCAACCCGGAAAGACACGACAAAACGCCAC
TGGCAGCAGCCATTAGTAACAGGAGTGCACGAGAAGATAGATTAAGAGGTCTTGAAGTAG
AGGCCTGACTGCGGCTACACTGAAAGAACAGTTTTGGTAATGGCGGTCTCGTGAACCCTG
TTACCGGGTTAAGCAGTTCCCCAACTGACTTAACCTTCGAACAAACCGCCTCCCCAGGCG
GTTTTTTCGTTTACAGAGCAAGAGATTACGATTCATTGAAAAGGATCTCAAGAAGATCCT
TTGTAGATTACTATCAATTAATCTTCCGAACATGACACCAGTCACTGTTGATTACGGTTA
AACCGCTCCGTAACAGGTTTCCCTCGTATTGGTGACTTGCAGCACCAAAGAAGCAAAAAA
GATAAATATATCTACTTATTGAGAGAT