package LIMS::Controller::Roles::ULISA;
use Moose::Role;
use Data::Dumper;
use IO::All;
use XML::Simple qw(:strict); # need to specify ForceArray & KeyAttr if using :strict here
use LIMS::Local::ScriptHelpers; # ftp_file
has script_helpers => ( is => 'ro', isa => 'LIMS::Local::ScriptHelpers',
lazy_build => 1 );
has xs_options => ( is => 'ro', isa => 'HashRef', lazy_build => 1 );
sub send_ulisa {
my ($self, $data) = @_; # warn Dumper $data;
# $self->_example_data(); # uncomment to dump data structure for example xml
my $xs = XML::Simple->new();
# options for XMLout (needs hash):
my %xs_opts = %{ $self->xs_options }; # warn Dumper $opts;
# munge $data into hashref format expected by XMLout:
my $ref = $self->_format($data);
my $input = { add => $ref }; # enclose xml in outer <add> block
my $xml_out = $xs->XMLout( $input, %xs_opts ); # warn Dumper $xml_out;
my %h = ( data => $ref, xml => $xml_out );
my $rtn = $self->_ftp_file(\%h);
}
sub _ftp_file {
my ($self, $args) = @_; # href (data href & xml str)
my $request_id = $args->{data}->{case}->{requestid};
my $content = $args->{xml}; # warn $content;
my $tools = $self->script_helpers(); # warn Dumper $tools;
my $cfg = $self->cfg('settings'); # warn Dumper $cfg;
my $filename = sprintf '%s.xml', $request_id;
my $src_path = '/tmp/' . $filename;
$content > io($src_path);
my %params = (
local_filename => $src_path,
remote_filename => $filename,
server_addr => $cfg->{dako_link_addr},
username => $cfg->{dako_link_user},
password => $cfg->{dako_link_pwd},
); # warn Dumper \%params;
# ftp file (returns str on failure, undef on success):
my $rtn = $tools->ftp_file(\%params);
if ($rtn) { # warn Dumper $rtn;
return $rtn;
}
else {
io($src_path)->unlink;
return 0;
}
}
sub _format { # returns hashref:
my $self = shift;
my $data = shift;
my $request = $data->{request};
my $patient = $data->{patient};
my $lab_test = $data->{lab_test};
my $now = LIMS::Local::Utils::time_now->epoch; # warn $now;
my @slides;
for my $ref (@$lab_test) { # warn Dumper $ref;
# create unique slide ID from request.id, test.id & epoch (max 32 chars):
my $slide_id = sprintf 'R%sT%sE%s',
$request->{id}, $ref->{test_id}, $now;
push @slides, {
slideid => $slide_id,
protocol => $ref->{test_name},
slidetype => 2, # IHC
};
}
my $lab_number = join '/',
$request->{request_number}, $request->{year} - 2000;
my %h; # hash data structure for input to XMLout
{
$h{case} = {
requestid => $request->{id},
firstname => $patient->{first_name},
lastname => $patient->{last_name},
caseid => $lab_number,
};
# add slides data:
$h{slides}{caseid} = $lab_number; # slides section needs caseid
$h{slides}{slide} = \@slides;
}; # warn Dumper \%h;
return \%h;
}
sub _example_data {
my $self = shift;
my $xs = XML::Simple->new();
my %opts = %{ $self->xs_options }; # warn Dumper $opts;
my $data; $data .= $_ for <DATA>; # warn $data;
my $foo = XMLin($data, ForceArray => 1, KeyAttr => []); warn Dumper $foo;
my $bar = $xs->XMLout( $foo, %opts ); warn Dumper $bar;
}
sub _build_xs_options {
my %opts = (
XMLDecl => q!<?xml version="1.0" encoding="UTF-8"?>!,
RootName => 'ulisa',
NoAttr => 1,
SuppressEmpty => 0, # ? only works for xml_in
KeyAttr => [],
);
return \%opts;
}
sub _build_script_helpers { LIMS::Local::ScriptHelpers->new }
1;
__DATA__
<add>
<case caseid="H12345678">
<firstname>Norbert</firstname>
<lastname>Colon</lastname>
</case>
<slides caseid="H12345678">
<slide>
<slideid>87</slideid>
<slidetype>2</slidetype>
<protocol>CD20</protocol>
</slide>
<slide>
<slideid>88</slideid>
<slidetype>2</slidetype>
<protocol>ki-67</protocol>
</slide>
</slides>
</add>