#!/usr/bin/perl
=begin
--------------------------------------------------------------------------------
generates XML data file for genomics data, ftp transfer
also transfers consent forms (or any file in request dir) with ctime within MAX_AGE
run from cron hourly, or change MAX_AGE
run as root/www-data or directory read permissions denied (on test server only ?)
--------------------------------------------------------------------------------
=cut
##############################################################
use constant MAX_AGE => 3600; # NEEDS TO BE SAME VALUE AS CRON
my $duration = $ARGV[0] || MAX_AGE; # say $duration; # seconds
my $JUST_TESTING = 1; # skips file transfer
##############################################################
use lib (
'/home/raj/perl5/lib/perl5',
'/home/raj/apps/HILIS4/lib',
'/home/raj/perl-lib', # Local::XMLSimple - patched to escape single-apostrophe
);
use LIMS::Local::ScriptHelpers;
use Local::XMLSimple qw(:strict); # need to specify ForceArray & KeyAttr if using :strict here
use Data::Printer alias => 'p', use_prototypes => 0;
use FindBin qw($Bin); # warn $Bin; exit;
use Modern::Perl;
use Path::Tiny;
use IO::All;
# get tools from LIMS::Local::ScriptHelpers:
my $tools = LIMS::Local::ScriptHelpers->new();
my $sql_lib = $tools->sql_lib();
my $dbix = $tools->dbix();
# switch to 'genomics' db:
$dbix->dbh->do('use `genomics`');
my %SQL = (
demographics => $sql_lib->retr('genomics_demographics'),
request_ids => $sql_lib->retr('genomics_requests'),
storage => $sql_lib->retr('genomics_storage'),
results => $sql_lib->retr('genomics_results'),
);
# get request ids:
my @request_ids = do {
my $sql = $SQL{request_ids};
# count number of placeholders in $sql:
my $n = () = $sql =~ /\?/g; # p $n;
# bind one $duration per placeholder:
my @bind = map $duration, (1..$n); # p \@bind;
$dbix->query( $sql, @bind )->flat; # array
}; # p \@request_ids; exit;
#===============================================================================
exit unless @request_ids;
#===============================================================================
my $cfg_file = "$Bin/../lib/settings.cfg";
my $settings = Config::Auto::parse($cfg_file); # p $settings;
my $timestamp = LIMS::Local::Utils::time_now();
use constant TMP_DIR => '/tmp'; # where to create temp data file
my @lab_sections = do {
my @args = ( 'lab_sections', ['section_name'], { is_active => 'yes'} );
$dbix->select(@args)->flat; # array
}; # p \@lab_sections;
# only need this if using xml element names for data feed:
# my $test_element_map = get_lab_test_to_xml_element_map(); # p $test_element_map; exit;
{ # go:
# get requests 1-to-1 data:
my @requests = $dbix->query( $SQL{demographics}, @request_ids )->hashes;
# p @requests;
for my $req (@requests) { # p $req; # get results data:
my $request_id = $req->{request_id};
# allocate GeL/participant id if screened:
if ( my $arm = $req->{arm} ) {
my $gel_id = ( lc $arm eq 'rare disease' )
? $request_id + 223000000
: $request_id + 122000000;
$req->{participant_id} = $gel_id;
} # p $req;
my %req_fields = map +($_ => $req->{$_}), # don't need request_num:
grep $_ !~ /request_number/, keys %$req; # p \@req_fields;
# build data structure for this request:
my %h = ( Demographics => \%req_fields ); # p \%h;
SECTION:
for my $section_name (@lab_sections) { # p $section_name;
# skip unless $section_name in $test_element_map keys:
# my $section_element_map = $test_element_map->{uc($section_name)}
# or next SECTION; # p $section_element_map;
my $data = do {
my @bind = ( $request_id, $section_name );
$dbix->query( $SQL{results}, @bind )->hashes;
}; # p $data;
RESULT: # each test/result pair for this section
for my $ref (@$data) { # hashref of keys: test_name & result
my $test_name = $ref->{test_name};
=begin # this is only needed to map test_names to GeL xml element names:
# get XML element name or skip test (not required in XML data):
my $element_name = $section_element_map->{$test_name}
or next RESULT; # p $element_name;
# add element name and result to section data:
$h{$section_name}{$element_name} = $ref->{result};
=cut
# if NOT using GeL xml element names:
$h{$section_name}{$test_name} = $ref->{result};
}
}
# fluidx storage (1-to-many with request_id):
if ( my @data = $dbix->query( $SQL{storage}, $request_id )->hashes ) {
$h{Storage}{Vials}{vial} = \@data; # p \@data;
}
{ # consent form filename (need to allow for >1 file):
my $filepath = get_destination_sub_dir($req); # p $filepath;
if ( -e $filepath ) {
my @contents = io($filepath)->all;
FILE:
for my $f (@contents) { # p $f;
next FILE unless $f->type eq 'file';
# add as array in case >1 file in dir
push @{ $h{Consent}{Files}{file} }, $f->filename;
my $file_age = ( $timestamp->epoch - $f->ctime ); # p $file_age; # in seconds
next if $file_age > MAX_AGE; # p [ $f->filename, $age ];
{ # transfer file (returns 0 if JUST_TESTING):
my %args = (
local_filename => $f->name,
remote_filename => $f->filename,
); # p \%args;
ftp_file(\%args);
}
}
}
}
{ # create xml file & send:
my $local_name = sprintf '%s_%s.xml',
$request_id, $timestamp->strftime('%Y_%m%d_%H%M%S'); # p $local_name;
my $full_path = join '/', TMP_DIR, $local_name; # p $full_path;
my $content = to_xml(\%h); # say $content;
$content > io($full_path);
{ # transfer file (returns 0 if JUST_TESTING):
my %args = (
local_filename => $full_path,
remote_filename => $local_name,
);
ftp_file(\%args);
}
}
}
}
#-------------------------------------------------------------------------------
sub ftp_file {
my $args = shift;
my $cfg = $settings->{ppm_server};
# modify destination_dir for genomics data:
my $remote_filename = join '/', 'HILIS_GEL', $args->{remote_filename};
my $local_filename = $args->{local_filename}; # p $local_filename;
my %params = (
local_filename => $local_filename,
remote_filename => $remote_filename,
server_addr => $cfg->{remote_address},
username => $cfg->{username},
password => $cfg->{password},
); # p \%params;
#===============================================================================
unless ($JUST_TESTING) {
# ftp file (returns str on failure, undef on success):
my $rtn = $tools->ftp_file(\%params); # p $rtn;
if ($rtn) { # p $rtn;
$tools->mail_admin({ script => $0, msg => $rtn });
warn "$0 - $rtn\n"; # dump to logs but don't die!!
}
}
#===============================================================================
{ # only delete xml file, not consent forms!!
my $tmp_dir = TMP_DIR; # p $tmp_dir; # TMP_DIR doesn't work used direct in regex
if ( $local_filename =~ m!^$tmp_dir/! ) { # say "deleting $local_filename";
# io($local_filename)->unlink; # switched off for testing
}
}
}
#-------------------------------------------------------------------------------
sub to_xml {
my $data = shift; # arrayref of request datasets
# options for XMLout (needs array or hash):
my %xs_opts = xs_options(); # p %xs_opts;
my $xs = Local::XMLSimple->new(%xs_opts);
my $ref = {
FileCreationDateTime => $timestamp->strftime('%F %T'),
# add direct if NOT using xml element names, otherwise use format_request():
# Record => format_request($data),
Record => $data,
};
# enclose xml in outer <add> block; add 'version' inline:
# my $input = { add => $ref, version => 2 };
my $xml_out = $xs->XMLout($ref); # p $xml_out;
return $xml_out;
}
#-------------------------------------------------------------------------------
sub xs_options {
my %opts = (
SuppressEmpty => 0, # ? only works for xml_in
NoEscape => 0, # should be default anyway, but doesn't work
RootName => 'HILIS4Genomics',
XMLDecl => q!<?xml version="1.0" encoding="UTF-8"?>!,
KeyAttr => [],
NoAttr => 1, # gives inline (scalar) AND nested (arrayref) attributes
);
return %opts;
}
#-------------------------------------------------------------------------------
# formats repeating request blocks (only needed if using xml element names):
sub format_request {
my $r = shift; # p $r;
my %data;
{ # registration/demographics:
my $ref = $r->{Demographics};
my %h = (
nhs_number => $ref->{nhs_number},
date_of_birth => $ref->{dob},
last_name => $ref->{last_name},
first_name => $ref->{first_name},
gender => $ref->{gender},
);
$data{Registration} = \%h;
} # p \%data;
return \%data;
}
#-------------------------------------------------------------------------------
sub get_lab_test_to_xml_element_map { # only needed if using xml element names
my @data = <DATA>; # p @data;
my %map;
for (@data) {
chomp; # say $_;
my ($section, $test_name, $element_name) = split ':', $_;
# p [$section, $test_name, $element_name];
next unless $section;
$map{$section}{$test_name} = $element_name;
} # p \%map;
return \%map;
}
#-------------------------------------------------------------------------------
sub get_destination_sub_dir {
my $ref = shift; # p $ref;
my ($year) = $ref->{registered} =~ m!^(\d{4})!; # not using requests.year
my $request_num = $ref->{request_number}; # p [$year, $request_num];
my $i = int ( $request_num / 100 ); # warn $i; # 1-99 = 0, 100-199 = 1, 200-299 = 2, etc
my $mini_dir = sprintf '%s-%s',
100 * $i || 1, # default to 1 if 0; 1, 100, 200, 300, etc
100 * $i + 99; # 99, 199, 299, etc
my $app_dir = path($tools->path_to_app_root)->realpath; # p $app_dir;
my $rel_path = 'static/files/genomics';
my $destination_dir = join '/', # eg /path/to/uploads/2013
$app_dir,
$rel_path,
$year,
$mini_dir,
$request_num; # p $destination_dir;
return $destination_dir;
}
# map of lab-section => test name => XML element name
__DATA__
CONSENT:consent_date:date-of-consent
CONSENT:consent_form_version:name-and-version-of-consent-form
CONSENT:consent_taken:consent-given
CONSENT:info_sheet_version:name-and-version-of-participant-information-sheet
CONSENT:consent_q1:consent-question-1
CONSENT:consent_q2:consent-question-2
CONSENT:consent_q3:consent-question-3
CONSENT:consent_q4:consent-question-4
CONSENT:consent_q5:consent-question-5
CONSENT:consent_q6:consent-question-6
CONSENT:consent_q7:consent-question-7
CONSENT:consent_q8:consent-question-8
CONSENT:consent_q9:consent-question-9
CONSENT:consent_q10:consent-question-10
CONSENT:consent_q11:consent-question-11
CONSENT:consent_q12:consent-question-12
CONSENT:consent_q13:consent-question-13
CONSENT:consent_q14:consent-question-14
SPECIMENS:edta1:DNA Blood Germline
SPECIMENS:pst:LiHep Plasma
SPECIMENS:paxgene_rna:RNA Blood
SPECIMENS:sst:Serum
SPECIMENS:handling_protocol:Laboratory Method
STORAGE:vial_id:Laboratory Sample ID
STORAGE:rack_id:GMC Rack ID
STORAGE:rack_location:GMC Rack Well
DNA:edta1_qc_date:Test Result DateTime
DNA:edta1_qc_type:Test Result Type
DNA:edta1_qc_result:Test Result Value
DNA:edta1_fluidx:Laboratory Sample ID
DNA:edta1_fluidx_vol:Laboratory Sample Volume
DNA:edta1_fluidx_rack_id:GMC Rack ID
DNA:edta1_fluidx_rack_well:GMC Rack Well
DNA:edta1_fluidx_vol:Laboratory Remaining Volume Banked
DISPATCH:consignment_number:GMC Sample Consignment Number
DISPATCH:dna_dispatched:GMC Sample Dispatch Date
DISPATCH:omics_dispatched:GMC Sample Dispatch Date
