G::Shell::EUtils - G-language Shell helper module for searching NCBI.

  This class is a part of G-language Genome Analysis Environment, 
  providing functions for searching NCBI with EUtilities.

    require LWP::UserAgent;

    my $db = shift;
    my $keyword = shift;

    unless(length($db) || $keyword){
	help('entrez');
	return;
    }

    unless($einfo{$db}){
	print STDERR "  Database\" $db\" is not available.\n";
	return;
    }

    my $ua = new LWP::UserAgent;

    my %params = (
		  email   => 'gaou@sfc.keio.ac.jp',
		  tool    => 'g-language.org',
		  db      => $db,
		  retmax  => 10,
		  retmode => 'xml',
		  term    => $keyword,
		  );

    my $url = $esearch . join('&', map {"$_=$params{$_}"} keys %params);

    my $request = new HTTP::Request('GET', $url);
    my $response = $ua->request($request);

    if ($response->is_success) {
	my $xml = XMLin($response->content);

	my $entryText = 'entries';
	$entryText = "entry" if ($xml->{Count} == 1);

	printf "    %d %s found in %s: (Showing up to 10 hits)\n\n", $xml->{Count}, $entryText, uc($db);

	my $id;
	if(ref($xml->{IdList}->{Id}) eq 'ARRAY'){
	    $id = join(',', @{$xml->{IdList}->{Id}});
	}else{
	    $id = $xml->{IdList}->{Id};
	}

	my %params = (
		      email   => 'gaou@sfc.keio.ac.jp',
		      tool    => 'g-language.org',
		      db      => $db,
		      retmax  => 10,
		      retmode => 'xml',
		      id      => $id,
		      );

	my $url = $esummary . join('&', map {"$_=$params{$_}"} keys %params);

	my $request = new HTTP::Request('GET', $url);
	my $response = $ua->request($request);

	if ($response->is_success) {
	    my $xml = XMLin($response->content);

	    my $i = 1;

	    if(ref($xml->{DocSum}) eq 'HASH'){
		my $entry = $xml->{DocSum};
		my %info;

		foreach my $item (@{$entry->{Item}}){
		    if($item->{Name} eq 'AuthorList'){
			if(ref($item->{Item}) eq 'HASH'){
			    $info{FirstAuthor} = $item->{Item}->{content};
			}else{
			    $info{FirstAuthor} = $item->{Item}->[0]->{content};
			}
		    }else{
			$info{$item->{Name}} = $item->{content};
		    }
		}
		
		if($db eq 'pubmed'){
		    printf "    %2d. PMID:   %s\n", $i, $entry->{Id};
		    printf "        %s et al.\" %s\"\n        %s  %s\n\n", $info{FirstAuthor}, $info{Title}, $info{Source}, $info{SO};
		}else{
		    printf "    %2d. Accession Number:   %s\n", $i, $info{Caption};
		    printf "        %s\n\n", $info{Title};
		}
	    }else{
		foreach my $entry (@{$xml->{DocSum}}){
		    my %info;
		    
		    foreach my $item (@{$entry->{Item}}){
			if($item->{Name} eq 'AuthorList'){
			    if(ref($item->{Item}) eq 'HASH'){
				$info{FirstAuthor} = $item->{Item}->{content};
			    }else{
				$info{FirstAuthor} = $item->{Item}->[0]->{content};
			    }
			}else{
			    $info{$item->{Name}} = $item->{content};
			}
		    }
		    
		    if($db eq 'pubmed'){
			printf "    %2d. PMID:   %s\n", $i, $entry->{Id};
			printf "        %s et al.\" %s\"\n        %s  %s\n\n", $info{FirstAuthor}, $info{Title}, $info{Source}, $info{SO};
		    }else{
			printf "    %2d. Accession Number:   %s\n", $i, $info{Caption};
			printf "        %s\n\n", $info{Title};
		    }
		    
		    $i ++;
		}
	    }
	} else {
	    print $response->error_as_HTML;
	}

    } else {
	print $response->error_as_HTML;
    }

    my $keyword = shift;

    unless($keyword){
	help('pubmed');
	return;
    }

    entrez('pubmed', $keyword);