#!/usr/bin/env perl
=begin
--------------------------------------------------------------------------------
generates NCRS XML data file for all authorised requests with diagnosis either
ICDO3 '/3', or 'see comments' with a non-null comment section, where authorisation
date or diagnosis revision date during previous 1 month
test mode skips file transfer & archive, dumps data to file (/tmp dir)
* results summaries combined with PathologyReportText until schema evolves to
accomodate them, then will need to revert as_cdata($result) & to_camel_case()
usage:
CENTRE=<centre> $0 [-m <months> - optional (defaults to 1)][-t - testing]
# scp /tmp/<filename> hmds@163.160.247.17:<filename> # broken
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!! for new server: need to manually ssh into server once to add key to known_hosts
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
online reference:
Using ICD-O-3 online: http://codes.iarc.fr/usingicdo.php
ICDO3 topographical codes: http://codes.iarc.fr/topography
ICDO3 morphological codes: http://codes.iarc.fr/codegroup/2
ICD-O-3 to ICD-10 conversion for hemato-oncological diseases:
<http://www.krebsdaten.de/Krebs/DE/Content/Publikationen/Poster/Downloads/2014/
hemato-oncological_diseases_classification_ottawa_engl.pdf?__blob=publicationFile>
All leukemias have a site-specific code of bone marrow (C42.1) except myeloid sarcoma
Multiple myeloma � code site to C42.1
RULE D. Topography codes for lymphomas: If a lymphoma involves multiple lymph node regions,
code to C77.8 (lymph nodes of multiple regions). Code extranodal lymphomas to the site of
origin, which may not be the site of the biopsy. If no site is indicated for a lymphoma,
code to C77.9 (lymph node, NOS). C80.9 if suspected to be extranodal but site is not stated.
--------------------------------------------------------------------------------
=cut
use Getopt::Std;
getopts('m:tq'); # months, testing, sql-trace
our($opt_m,$opt_t,$opt_q); # warn $opt_m; exit;
use strict;
use warnings;
use lib '/home/raj/perl5/lib/perl5';
# File::Spec 3.40 required in a ScriptHelpers dependency, so load before charnames
# or cron loads system File::Spec 3.33:
use File::Spec 3.40;
use charnames ':full'; # for perl < 5.16 - to use unicode names (eg LINE FEED)
use Encoding::FixLatin qw/fix_latin/;
use IPC::System::Simple qw(capture);
use Data::GUID qw(guid_string);
use XML::Simple qw(:strict); # need to specify ForceArray & KeyAttr if using :strict here
use XML::SAX::ParserFactory;
use XML::Validator::Schema;
use XML::Compile::Schema;
use SQL::Abstract::More;
use Data::Printer;
use Config::Auto;
use Modern::Perl;
use XML::LibXML;
use Try::Tiny;
use Template;
use DateTime; # last_day_of_month()
use IO::All -utf8; # fix for "Wide character in print"
use FindBin qw($Bin); # warn $Bin;
use lib $Bin . '/../../../lib';
use LIMS::Local::ScriptHelpers;
use lib '/home/raj/perl-lib';
use Local::DB; # switch off date auto-inflation:
$Local::DBIx::Simple::Result::NO_AUTO_DATE_INFLATION = 1;
my $centre = $ENV{CENTRE} || die 'no centre param supplied';
#===============================================================================
my $JUST_TESTING = $opt_t || 0; # skips file transfer & file archive
my $duration = $opt_m || 1; # months ago
my $new_line_marker = '[~~]'; # using CDATA now
#===============================================================================
$ENV{SQL_TRACE} = $opt_q;
# supply 'SuppressEmpty' arg (1 or undef) to XMLOut: ---------------------------
=begin
# SuppressEmpty => 1:
<Address>
<UnstructuredAddress />
</Address>
# SuppressEmpty => undef:
<Address>
<UnstructuredAddress>
<streetAddressLine></streetAddressLine>
</UnstructuredAddress>
</Address>
=cut
my $suppress_empty = 1; # options 1 or undef to suppress warning, 0 gives warning
#-------------------------------------------------------------------------------
my $cfg_file = "$Bin/../lib/settings.cfg";
my $settings = Config::Auto::parse($cfg_file); # p $settings;
my $ncrs_cfg = $settings->{ncrs_data}->{$centre}
|| die "can't find settings for $centre in $cfg_file"; # p $ncrs_cfg;
# organisation code where service (HMDS, NBT, UCLH, etc) located:
my $service_org_code = $ncrs_cfg->{org_code}
|| die 'service org code not configured';
my $hmds_org_code = 'RR8F4'; # apparently
# get tools from LIMS::Local::ScriptHelpers:
my $tools = LIMS::Local::ScriptHelpers->new();
my $config = $tools->config();
my $dbname = $centre eq 'leeds' ? 'hilis4' : $centre;
my $dbix = Local::DB->dbix({ dbname => $dbname }); # warn $dbix->dbh->{Name};
# schema definition for validation and XML::Compile::Schema/XML::LibXML method:
my $xsd = '/home/raj/apps/HILIS4/setup/schema/xsd/ncrs.xsd';
# dates ========================================================================
my $timestamp = $tools->time_now->datetime;
# get date last month - handles BST:
my $ref_date = $tools->date_subtract(months => $duration);
# format for ReportingPeriodStartDate & ReportingPeriodEndDate
my $start_date = $ref_date->strftime('%Y-%m-01');
my $end_date = DateTime->last_day_of_month(
year => $ref_date->year,
month => $ref_date->month,
)->ymd; # p $start_date; p $end_date;
# ==============================================================================
my @lab_sections = $dbix->select('lab_sections','section_name')->column;
# remove non-word chars to match result_summary data from get_data_map():
$_ = to_camel_case($_) for @lab_sections; # p @lab_sections; exit;
# The submission file must be named using the following convention:
# COSD_<FILE SOURCE>_<Submitting Org>_<Reporting Period Start Date>_
# <Reporting Period End Date>_<Date of file creation>.xml
my $data_filename = sprintf 'COSD_PATH_%s_%s_%s.xml',
$service_org_code, $start_date, $end_date; # p $data_filename;
# $data_filename = 'hmds_test_cosd.xml';
my @skip_screens = ( # not very maintainable as new ones added!!
'Inappropriate/unsuitable sample',
'Inappropriate MPN request',
'Rituximab (RA) monitoring',
'Follow-up CML (PB)',
'Follow-up CML (BM)',
'Chimerism (CHIA/CHIB)',
'Chimerism (CHIM)',
'HIV monitoring', # discontinued Feb/2016
'NCG PNH (PB)', # discontinued 03/2019
'PNH NCG (PB)', # new term 03/2019
'NCG PNH (BM)',
'Outreach',
);
# exclude anonymised clinical trials:
my @anonymised_trials = (
'HTG RCODOXM/IVAC',
'Archigen AGB002',
'AUTOLUS AUTO2-MM1',
'NCRI INCA',
'PenCTU ENRICH',
'Roche Gallium',
'Unknown/other' # some have anonymised names
);
use constant TMP_DIR => '/tmp'; # where to create temp data file
my %all_guids; # GUID counter to ensure uniqueness
my @data = (); # global !!
{ # go:
# get requests 1-to-1 data:
my @requests = do {
my ($sql, @bind) = _ncrs_data();
$dbix->query($sql, @bind)->hashes;
}; # p @requests; exit;
my @request_ids = map $_->{request_id}, @requests; # p @request_ids;
# get data maps of vertical tables - much faster than tying into main query:
my $data_map = get_data_map(\@request_ids); # p $data_map;
for my $r (@requests) { # p $r; next;
my $request_id = $r->{request_id};
# merge vertical table data with $r:
my $vars = combine_data($r, $data_map->{$request_id});
push @data, $vars;
} # p @data;
}
# enable hash counter in new_guid() for debugging:
say "$_ is not unique" for grep { $all_guids{$_} > 1 } keys %all_guids;
{ # create output file & push to remote server:
my $file_path = join '/', TMP_DIR, $data_filename;
# generate xml (validation failure warns error & returns 0):
if ( my $content = to_xml() ) { # p $content;
$content > io($file_path);
# transfer file:
unless ($JUST_TESTING) {
my %args = ( local_filename => $file_path );
transfer_file(\%args);
}
}
}
#-------------------------------------------------------------------------------
sub to_xml {
my $count = @data; # p $count;
my $ref = {
OrganisationIdentifierCodeOfSubmittingOrganisation => { # always Leeds/HMDS:
extension => $hmds_org_code,
},
Id => { root => new_guid() }, # returns new Data::GUID as_string
RecordCount => { value => $count },
ReportingPeriodStartDate => $start_date,
ReportingPeriodEndDate => $end_date,
FileCreationDateTime => $timestamp,
}; # p $ref;
my $xml_out =
#xml_simple($ref); # XML::Simple method
#xml_libxml($ref); # XML::LibXML method
xml_template($ref); # TT method (provides easiest layout control)
# hack to add namespace data (don't need this for TT method):
# chomp( my $namespace = namespace_data() ); # remove trailing new-line
# $xml_out =~ s/(COSD:COSD)/$1\n$namespace/; # don't use 'g', only want start-tag
# p $xml_out;
{ # validate xml:
# switch debug on to show data structure:
my $validator = XML::Validator::Schema->new(file => $xsd, debug => 0); # p $validator;
my $parser = XML::SAX::ParserFactory->parser(Handler => $validator);
my $err;
try { $parser->parse_string($xml_out) }
catch { $err = $_ };
if ($err) {
warn $err;
return 0;
}
}
return $xml_out;
}
#-------------------------------------------------------------------------------
# formats repeating COSDRecord blocks:
sub format_cosd_unit {
my $v = shift;
my %COSDRecord = (
Id => {
root => new_guid(), # returns new Data::GUID as_string
},
);
my %HAEM;
{ # COSDRecord/Haematology/HaematologyCore:
my $labno = $ncrs_cfg->{labno_prefix}
. $v->{request_number} . '/' . ( $v->{year} - 2000 );
# NHSNumberStatusIndicator = "Number present but not traced (02)"
# OR "Number not present and trace not required (07)":
my $NHSNumberStatusIndicator = defined $v->{nhs_number} ? '02' : '07';
my %h = (
HaematologicalCoreLinkagePatientId => {
NHSNumber => {
extension => $v->{nhs_number},
},
NHSNumberStatusIndicator => {
code => $NHSNumberStatusIndicator,
},
LocalPatientIdExtended => $v->{unit_number},
Birthdate => $v->{dob},
OrganisationIdentifierCodeOfProvider => {
extension => $v->{organisation_code},
},
},
HaematologicalCoreDemographics => {
PersonFamilyName => {
family => $v->{last_name},
},
PersonGivenName => {
given => given_name($v),
},
Address => {
UnstructuredAddress => {
streetAddressLine => $v->{address},
},
},
Postcode => {
postalCode => $v->{post_code},
},
Gender => {
code => gender_code($v->{gender}),
},
},
HaematologicalCorePathology => {
OrganisationSiteIdentifierOfPathologyTestRequest => {
extension => $v->{organisation_code}
},
OrganisationIdentifierOfReportingPathologist => {
extension => $service_org_code
},
PathologistConsultantCode => {
extension => to_gmc($v->{reporter_code})
},
PathTestReqCareProfCode => {
extension => to_gmc($v->{referrer_code})
},
MorphologySNOMEDPathology => { # ICDO3
code => icdo3_to_snomed($v->{icdo3})
},
# could also use:
# <MorphologySNOMEDDiagnosis code="M98233" />
# <MorphologyICDODiagnosis code="M98233" />
ServiceReportStatus => {
code => report_status($v->{diagnosis})
},
InvestigationResultDate => $v->{authorisation_date},
PathologyReportText => free_text_report($v),
SampleCollectionDate => $v->{sample_date},
# SampleReceiptDate => $v->{request_date}, # moved below ...
ServiceReportId => { extension => $labno },
# morphology code if needed is 3 or 1 (from ICDO3 /3 or /1 suffix)
# useless for haematology - refers to solid tumours:
# 1 = primary, 4 = region LN, 5 = metastatic, 9 = not known
# SpecimenNature => { code => 9 },
# One of TOPOGRAPHY (SNOMED), TOPOGRAPHY (SNOMED CT) or PRIMARY
# DIAGNOSIS (ICD PATHOLOGICAL) is required for the schema. It is
# expected that most submissions will include TOPOGRAPHY (SNOMED).
# PRIMARY DIAGNOSIS (ICD PATHOLOGICAL) is the PRIMARY DIAGNOSIS
# based on the evidence from a pathological examination. Format
# CXX.X or DXX.X
# PrimaryDiagnosisICDPath => sample_to_snomed($v),
# topography code (primary site of origin): suspended
# TopographySNOMEDPathology => { code => topography_code($v) },
},
);
# only require one of SampleCollectionDate / SampleReceiptDate:
unless ( $v->{sample_date} ) {
my $ReceiptDate = $v->{request_date};
$h{HaematologicalCorePathology}{SampleReceiptDate} = $ReceiptDate;
}
$HAEM{HaematologicalCore} = \%h;
}
# lab results not part of v8 schema (temporarily combined with PathologyReportText):
# { # COSDRecord/Haematology/HaematologyContent/LaboratoryResults:
# my %h = map +( $_ => $v->{$_} ), @lab_sections;
# $HAEM{HaematologicalContent}{LaboratoryResults} = \%h;
# }
$COSDRecord{Haematological} = \%HAEM;
return \%COSDRecord;
}
=begin
sub xml_simple { # XML::Simple (doesn't support ordered elements without hack)
my $ref = shift;
# options for XMLout (needs array or hash):
my %xs_opts = xs_options(); # p %xs_opts;
my $xs = XML::Simple->new(%xs_opts);
my $xml_out = $xs->XMLout($ref); # p $xml_out;
{ # get repeating COSDRecords (horrible hack because XML::Simple doesn't
# support ordered elements, create 2nd xml document and splice into outer one:
my %xs_opts = xs_options(); # p %xs_opts;
$xs_opts{RootName} = undef; # suppress, don't want outer xml element
delete $xs_opts{XMLDecl}; # delete, don't need for COSDRecord elements
my $xs = XML::Simple->new(%xs_opts); # p %xs_opts;
my @COSDRecords = map format_cosd_unit($_), @data; # p @COSDRecords;
my $records = $xs->XMLout({ COSDRecord => \@COSDRecords }); # p $records;
# splice in cosd records:
$xml_out =~ s{(</COSD:COSD>)}{$records . $1}e;
}
return $xml_out
}
sub xml_libxml { # XML::LibXML method
my $ref = shift;
push @{ $ref->{COSDRecord} }, format_cosd_unit($_) for @data; # p $ref;
# schema created from dummy xml by https://www.freeformatter.com/xsd-generator.html#ad-output
# had to change COSD:COSD in xml to COSD or outer element skipped:
my $schema = XML::Compile::Schema->new($xsd); # p $schema;
# see what types are defined
# $schema->printIndex; # exit;
# p $schema->template('PERL' => 'COSD'); exit;
# create and use a writer
my $write = $schema->compile(WRITER => 'COSD');
my $doc = XML::LibXML::Document->new('1.0', 'UTF-8');
my $xml = $write->($doc, $ref);
$doc->setDocumentElement($xml);
# show result
my $xml_out = $doc->toString(1);
# change COSD to COSD:COSD (as colon not supported in xsd):
# "error: field name contains 'COSD:COSD' which is not a valid NCName at COSD:COSD"
$xml_out =~ s/COSD(?!Record)/COSD:COSD/g; # match <COSD> but not <COSDRecord>
return $xml_out;
}
=cut
sub xml_template { # TT method:
my $ref = shift;
push @{ $ref->{COSDRecord} }, format_cosd_unit($_) for @data;
my %args = (
INCLUDE_PATH => ['/home/raj/apps/HILIS4/templates/cron'],
# ENCODING => 'utf8', # not sure it's needed
);
my $xml_out;
my $tt = Template->new(\%args);
$tt->process('ncrs_cosd.tt', { data => $ref }, \$xml_out)
or die $tt->error();
return $xml_out;
}
#-------------------------------------------------------------------------------
sub report_status { # 1 = Final (Complete); 2 = Preliminary (Interim)
my $diagnosis = shift; # p $diagnosis;
my @interim_terms = (
'awaiting final (diagnosis|review)',
'interim result', # NBT
);
return ( grep { lc $diagnosis =~ /^$_/ } @interim_terms ) ? 2 : 1;
}
#-------------------------------------------------------------------------------
# free-text specimen/biopsy_site/morphology/comment, etc:
sub free_text_report {
my $vars = shift; # p $vars;
my @rows;
push @rows, ( 'SPECIMEN(S): ' . $vars->{specimen_decode} );
if ( my $biopsy_site = $vars->{biopsy_site} ) {
push @rows, ( 'ANATOMICAL SITE(S): ' . $biopsy_site );
}
push @rows, ( 'SPECIMEN QUALITY: ' . $vars->{specimen_quality} );
if ( my $gross_desc = $vars->{gross_description} ) {
push @rows, ( 'GROSS DESCRIPTION: ' . $gross_desc );
}
if ( my $details = $vars->{clinical_details} ) {
push @rows, ( 'CLINICAL DETAILS: ' . $details );
}
for my $section (@lab_sections) { # p $section; # results summaries:
my $summary = $vars->{$section} || next; # p $summary;
# next unless $section eq 'haematology';
push @rows, ( join ': ', uc $section, $summary . "\n" );
}
if ( my $morphology = $vars->{morphology} ) {
push @rows, ( 'MORPHOLOGY: ' . $morphology );
}
if ( my $comment = $vars->{comment} ) {
push @rows, ( 'COMMENT: ' . $comment );
}
push @rows, ( 'DIAGNOSIS: ' . $vars->{diagnosis} );
push @rows, (
'REPORTED BY: ' . $vars->{reporter_name}
. ' on ' . $vars->{report_datetime}
);
my $str = join "\n", @rows;
# convert all non-utf8 chars (eg pasting from Word):
my $utf8_text = fix_latin($str);
# enclose text in CDATA tags:
return as_cdata($utf8_text);
}
#-------------------------------------------------------------------------------
# merge vertical table data with $vars
sub combine_data {
my ($vars, $supplimentary_data) = @_; # p $supplimentary_data;
{ # add data-map fields:
# result summaries (enclose text in CDATA tags):
for (@lab_sections) {
my $result = $supplimentary_data->{result_summary}->{$_} || next; # can't be '0'
# temporarily combined with PathologyReportText so doesn't need to be CDATA:
$vars->{$_} = $result; # as_cdata($result);
}
# reporter:
$vars->{$_} = $supplimentary_data->{reporter_data}->{$_},
for qw(reporter_name reporter_code report_datetime);
# specimen code(s) & decode(s):
$vars->{specimen_code}
= $supplimentary_data->{specimen}->{specimen_code};
$vars->{specimen_decode}
= $supplimentary_data->{specimen}->{description};
} # p $vars;
$vars->{gender} ||= 'U'; # p $vars;
return $vars;
}
#-------------------------------------------------------------------------------
sub topography_code {
my $vars = shift;
# C80.9 / Unknown primary site:
return 'C80.9' unless $vars->{icdo3};
my ($icdo3) = $vars->{icdo3} =~ /^(\d{4})/; # capture 1st 4 digits;
# plasmacytomas? CLL? EMZL? - check the MZL & MYD88-mutated entries!!
my %topo_code = (
8720 => 'C44._', # metastatic melanoma
9689 => 'C42.2', # splenic MZL
9699 => 'C80.9', # extranodal MZL (Rule D)
9700 => 'C44._', # MF
9709 => 'C44._', # cuteneous TCL
9718 => 'C44._', # primary cuteneous CD30+ LPD
# 9731 => 'C40._', # plasmacytoma (only of bone; C40 is bones, joints, etc)
9732 => 'C42.1', # myeloma
9733 => 'C42.1', # plasma-cell leukaemia
);
return $topo_code{$icdo3} if $topo_code{$icdo3};
# primary non-haematological tumour/metastatic carcinoma:
return 'C80.9' if in_num($icdo3, 8000, 8010);
# rhabdomyosarcoma/pnet/neuroblastoma:
return 'C80.9' if in_num($icdo3, 8900, 9260, 9500);
# mastocytosis, histiocytosis, langerhans:
return 'C80.9' if between($icdo3, 9741 => 9755);
# lymphomatoid granulomatosis, amyloidosis:
return 'C80.9' if between($icdo3, 9766 => 9769);
# Rule E: all leukaemias (9801/3 .. 9989/3):
return 'C42.1' if between($icdo3, 9801 => 9990);
# Rule D: default for lymphomas (9591/3 .. 9739/3)
return 'C77._' if between($icdo3, 9591 => 9739);
# escaped all above returns so output for debugging:
p $vars->{diagnosis};
}
#-------------------------------------------------------------------------------
sub between { # adapated from Acme::Tools
my ($test, $lower, $upper) = @_;
return $lower < $upper
? $test >= $lower && $test <= $upper
: $test >= $upper && $test <= $lower;
}
#-------------------------------------------------------------------------------
sub in_num { # lifted from Acme::Tools
my $val = shift || return 0; # shift 1st val, remaining in @_
for (@_) { return 1 if $_ == $val }
return 0;
}
#-------------------------------------------------------------------------------
sub icdo3_to_snomed { # eg 9960/3 -> M99603
local $_ = shift || return undef; # p $icdo3;
s{/}{}; # remove slash
return 'M' . $_;
}
#-------------------------------------------------------------------------------
sub gender_code {
my $gender = shift;
return 1 if lc $gender eq 'm';
return 2 if lc $gender eq 'f';
return 9; # x = not known, 9 = not specified
}
#-------------------------------------------------------------------------------
# first + optional middle names
sub given_name {
my $vars = shift;
return join ' ', grep $_, @{$vars}{ qw/first_name middle_name/ };
}
#-------------------------------------------------------------------------------
sub xs_options {
my %opts = (
SuppressEmpty => $suppress_empty,
RootName => 'COSD:COSD',
NoEscape => 1, # to preserve <!CDATA[..]]> tags
XMLDecl => q!<?xml version="1.0" encoding="UTF-8"?>!,
KeyAttr => [],
NoAttr => 1, # gives inline (scalar) AND nested (arrayref) attributes
);
return %opts;
}
#-------------------------------------------------------------------------------
#
sub transfer_file { # only called if not $JUST_TESTING
my $args = shift;
=begin scp function broken, replaced by email 07/2016
my $cfg = $settings->{nycris_server};
my %params = (
local_filename => $args->{local_filename},
server_addr => $cfg->{remote_address},
username => $cfg->{username},
password => $cfg->{password},
); # p %params;
# scp file (returns str on failure, undef on success):
# my $rtn = $tools->scp_file(\%params);
=cut
my $rtn = email_file(); # from 05/07/2016
my $script = $tools->script_filename;
if ($rtn) {
$tools->mail_admin({ script => $0, msg => $rtn });
warn "$script - $rtn\n"; # dump to logs but don't die!!
}
else {
archive_and_delete_file($args->{local_filename});
my $month = $ref_date->month_name; # for cron log:
print "$script reports $centre data for $month successfully dispatched\n";
}
}
#-------------------------------------------------------------------------------
sub email_file { # email a password-protected file:
# $data_filename too long for use as subject - capture org-code_year-month:
my ($subject) = $data_filename =~ /(COSD_PATH_\w{5}_\d{4}-\d{2})/;
# create file id from organisation code & date, for use as zip filename & pwd:
my ($file_id) = $subject =~ /(\w{5}_\d{4}-\d{2})/; # p $file_id;
my $password = ucfirst lc $file_id; # p $password;
my $zip_filename = lc $file_id . '.zip'; # p $zip_filename;
my @cmd = ('/usr/bin/zip');
push @cmd, '-q'; # quiet
push @cmd, '-j'; # junk dir name
push @cmd, ( '--password', $password );
# --------------------------------------------------------------------------
push @cmd, '-'; # only needed to allow piping of content if using capture()
# --------------------------------------------------------------------------
push @cmd, TMP_DIR . '/' . $zip_filename;
push @cmd, TMP_DIR . '/' . $data_filename; # p @cmd;
# override local centre service email with HMDS nhs.net address:
$config->{service_email} = 'hmds.lth@nhs.uk'; # p $config;
=begin # method to save zip file to disk & then use io() for $content:
# system(@cmd);
# my $content = io->file(TMP_DIR . '/' . $zip_filename)->all;
=cut
# use IPC::System::Simple to capture zip output:
my $content = capture(@cmd);
my %mail = (
config => $config,
subject => $subject,
filename => $zip_filename,
attachment => $content,
); # p %mail; # p @recipients;
my $ok = $tools->send_mail(\%mail, [ $ncrs_cfg->{recipient} ]); # returns 0 if msg fails
# for compatibility with scp_file():
return 'message(s) failed to send' if not $ok;
return 0; # don't return true unless msg fails
}
#-------------------------------------------------------------------------------
# archive data file (only called if not $JUST_TESTING):
sub archive_and_delete_file {
my $src_file = shift; # p $src_file;
my $path_to_archive = $settings->{nycris_server}->{path_to_archive};
# $data_filename too long - capture org-code_year-month:
my ($archive_filename) = $data_filename =~ /COSD_PATH_(\w{5}_\d{4}-\d{2})/;
# make sure it exists otherwise get error trying to tar non-existant file
if (-e $src_file ) { # warn 'it exists';
my $tar_file = sprintf '%s/%s.tar',
$path_to_archive, $archive_filename; # p $tar_file;
chdir TMP_DIR; # so we can use relative path for source directory
system( sprintf 'tar -cf %s %s', $tar_file, $data_filename ); # using relative $data_file.* not full path
system( sprintf "gzip $tar_file" ); # compress tar file
# delete source file:
io($src_file)->unlink;
}
}
#-------------------------------------------------------------------------------
sub get_data_map {
my $request_ids = shift; # p $request_ids;
my $map = {};
{ # request_specimens:
my $result = do {
my ($sql, @bind) = _request_specimens($request_ids);
$dbix->query($sql, @bind);
};
while ( my $vars = $result->hash ) { # p $vars;
my $request_id = $vars->{request_id};
my %data = (
specimen_code => $vars->{code},
description => $vars->{description},
); # p %data;
$map->{$request_id}->{specimen} = \%data;
}
}
{ # reporter data:
my $result = do {
my ($sql, @bind) = _reporters($request_ids);
$dbix->query($sql, @bind);
};
while ( my $vars = $result->hash ) { # p $vars;
my $request_id = $vars->{request_id};
my $reporter = join ' ',
ucfirst $vars->{first_name},
ucfirst $vars->{last_name};
my $reporter_code = $vars->{registration_number} || 'H9999998'; # OTHER HEALTH CARE PROFESSIONAL;
my %data = (
reporter_name => $reporter,
reporter_code => $reporter_code,
report_datetime => $vars->{report_datetime},
); # p %data;
$map->{$request_id}->{reporter_data} = \%data;
}
}
{ # result summaries:
my $result = do {
my ($sql, @bind) = _result_summaries($request_ids);
$dbix->query($sql, @bind);
};
while ( my $vars = $result->hash ) { # p $vars;
my $request_id = $vars->{request_id};
my $section = to_camel_case($vars->{section_name});
my $result = fix_latin($vars->{results_summary});
$map->{$request_id}->{result_summary}->{$section} = $result;
} # p $map->{result_summary};
} # p $map;
return $map;
}
#-------------------------------------------------------------------------------
sub tidy { # not in use, replaced by as_cdata()
my $str = shift; # p $str;
# trim:
$str =~ s/\A\s+//; # leading
$str =~ s/\s+\Z//; # trailing
#$str =~ s/\r?\n/$new_line_marker/g; # captures both \r\n & \n
$str =~ s/\N{CARRIAGE RETURN}?\N{LINE FEED}/$new_line_marker/g;
}
#-------------------------------------------------------------------------------
# need to use XML::Simple opt NoEscape => 1 to preserve CDATA tags:
sub as_cdata {
my $str = shift;
# 1) for XML::Simple
# return "<![CDATA[\n$_[0]\n]]>";
# 2) for XML::LibXML and Template methods:
my $cdata = XML::LibXML::CDATASection->new($str); # p $cdata->textContent;
return $cdata;
}
#-------------------------------------------------------------------------------
sub to_camel_case {
my $ref = shift; # p $ref;
$ref =~ s/_/ /g; # convert underscores to spaces for camelCasing
# now temporarily combined with PathologyReportText so don't need this yet:
# $ref = join '', map { ucfirst $_ } split '\W', $ref; # p $ref;
return $ref;
}
#-------------------------------------------------------------------------------
sub to_gmc { # only GMC codes permitted (CS codes under consideration):
my $reg_num = shift;
# $reg_num = 'H9999998' unless $reg_num =~ /^[CH]\d{7}$/; # handled at PHE now
return $reg_num;
}
#-------------------------------------------------------------------------------
sub namespace_data { # TODO: confirm uri's
return <<EOF
xmlns:COSD="http://www.datadictionary.nhs.uk/messages/COSDPathology-v8-1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
EOF
# xsi:schemaLocation="http://www.datadictionary.nhs.uk/messages/COSDPathology-v8-1
# COSDCOSDXMLSchema-v8-1.xsd"
}
#-------------------------------------------------------------------------------
sub new_guid {
my $guid = guid_string();
# $all_guids{$guid}++; # for debugging - to ensure uniqueness
return $guid;
}
# SQLA -------------------------------------------------------------------------
sub _ncrs_data {
my $report_status = $ncrs_cfg->{report_status};
my @cols = ( qw/
DISTINCT(r.id)|request_id
DATE(r.created_at)|request_date
r.request_number
r.year
p.last_name
p.first_name
p.middle_name
p.nhs_number
pc.unit_number
p.dob
p.gender
pd.address
pd.post_code
ref.national_code|referrer_code
rs.organisation_code
rr.biopsy_site
rr.gross_description
rr.specimen_quality
DATE(rr.specimen_date)|sample_date
rr.clinical_details
rr.morphology
rr.comment
d.name|diagnosis
d.icdo3
DATE(rh.time)|authorisation_date
/ );
my @rels = (
'requests|r' => q{r.patient_case_id=pc.id} ,
'patient_case|pc' => q{pc.patient_id=p.id} ,
'patients|p' => q{r.referrer_department_id=rd.id} ,
'referrer_department|rd' => q{rd.referrer_id=ref.id} ,
'referrers|ref' => q{pc.referral_source_id=rs.id} ,
'referral_sources|rs' => q{rh.request_id=r.id} ,
'request_history|rh' => q{rr.request_id=r.id} ,
'request_report_view|rr' => q{rr.diagnosis_id=d.id} ,
'diagnoses|d' => q{ris.request_id=r.id} ,
'request_initial_screen|ris' => q{ris.screen_id=s.id} ,
'screens|s' => q{=>rdh.request_id=r.id} ,
'request_diagnosis_history|rdh' => q{=>pd.patient_id=p.id} ,
'patient_demographics|pd' => q{=>rt.request_id=r.id} ,
'request_trial|rt' => q{=>rt.trial_id=ct.id} ,
'clinical_trials|ct'
);
# local_network_locations:
push @rels, ( 'lnl.parent_id=rs.parent_organisation_id' =>
'local_network_locations|lnl' ) if $centre eq 'leeds';
my %where = (
-and => [
{ # is reported/authorised & not excluded screens or [CN]EQAS cases:
# 'p.first_name' => { -not_like => '_' }, # some are valid records
-and => [
'p.last_name' => { -not_rlike => '[cn]qas' },
'p.last_name' => { -not_like => '_' },
],
'rh.action' => $report_status,
's.description' => { -not_in => \@skip_screens },
# 'r.id' => { -in => [353199, 353081] }, # force specific requests
},
-or => [ # reported/authorised or diagnosis history dates:
{
'MONTH(rh.time)' => $ref_date->month,
'YEAR(rh.time)' => $ref_date->year,
},
{
'MONTH(rdh.time)' => $ref_date->month,
'YEAR(rdh.time)' => $ref_date->year,
},
],
#===============================================================================
# all requests with ICDO3 /3 diagnosis:
'd.icdo3' => { -like => '%3' },
# any request (with/without icdo3, or clinical trial WITH icdo3):
# -or => [ # all non-trial cases OR clinical trial with ICDO3 diagnosis
# 'rt.request_id' => undef,
# 'd.icdo3' => { -not => undef },
# ],
# diagnosis not MGUS, or is 'see coments' with rr.comment - only
# makes sense if combined with "d.icdo => { -not undef }"
# -or => [
# 'd.name' => { '-not_rlike' => 'MGUS' },
# {
# 'd.name' => 'see comments',
# 'rr.comment' => { '!=' => undef }
# },
# ],
#===============================================================================
-or => [ # if trial, not an anomimised one
'ct.trial_name' => undef,
'ct.trial_name' => { -not_in => \@anonymised_trials },
],
-not => { # diagnosis = 'see comments' and comment is null
'rr.comment' => undef,
'd.name' => 'see comments',
},
],
);
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
-order_by => 'r.id',
# -limit => 1, # for testing
# -offset => 15,
); # p @args;
my ($sql, @bind) = SQL::Abstract::More->new->select(@args); # p $sql; p \@bind;
# $dbix->dump_query($sql, @bind); exit;
return ($sql, @bind);
}
sub _request_specimens {
my $request_ids = shift;
my @cols = (
'rs.request_id',
"GROUP_CONCAT(s.description separator '; ')|description",
'GROUP_CONCAT(s.sample_code)|code',
);
my @rels = ( 'request_specimen|rs', 'rs.specimen_id=s.id', 'specimens|s' );
my %where = ( 'rs.request_id' => { -in => $request_ids } );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
-group_by => 'rs.request_id',
); # p @args;
# need to supply our own injection_guard to override built-in sql injection
# attack prevention which detects ';' in GROUP_CONCAT, but we don't need one
# here as we have no user input:
my $sqla = SQL::Abstract::More->new( injection_guard => qr/^$/ );
my ($sql, @bind) = $sqla->select(@args); # p $sql; p \@bind;
# $dbix->dump_query($sql, @bind); exit;
return ($sql, @bind);
}
sub _reporters {
my $request_ids = shift;
my @cols = qw(
rh.request_id
rh.time|report_datetime
u.username
u.first_name
u.last_name
ur.registration_number
);
my @rels = (
'request_history|rh' => 'rh.user_id=u.id',
'users|u' => '=>ur.user_id=u.id',
'user_registration|ur'
);
my %where = (
'rh.request_id' => { -in => $request_ids },
'rh.action' => 'reported',
);
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
); # p @args;
my ($sql, @bind) = SQL::Abstract::More->new->select(@args); # p $sql; p \@bind;
# $dbix->dump_query($sql, @bind); exit;
return ($sql, @bind);
}
sub _result_summaries {
my $request_ids = shift;
my @cols = qw(
rs.request_id
rs.results_summary
ls.section_name
);
my @rels = qw(
request_result_summaries|rs rs.lab_section_id=ls.id lab_sections|ls
);
my %where = ( 'rs.request_id' => { -in => $request_ids } );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
); # p @args;
my ($sql, @bind) = SQL::Abstract::More->new->select(@args); # p $sql; p \@bind;
# $dbix->dump_query($sql, @bind); exit;
return ($sql, @bind);
}
#-------------------------------------------------------------------------------
=begin # not mapping samples to snomed
# decode for biopsy_site info:
my $anatomical_site_map =
$dbix->select('anatomical_sites', [qw(site_name snomed)])->map;
# p $anatomical_site_map;
sub sample_to_snomed {
my $vars = shift;
my @snomed;
# get info from biopsy_site if available, otherwise specimen code(s):
if ( my $biopsy_site = $vars->{biopsy_site} ) { # optional
my @sites = split '; ', $biopsy_site; # maybe multiple
push @snomed, $anatomical_site_map->{$_} for @sites;
}
else {
my @specimens = split ',', $vars->{specimen_code};
push @snomed, $specimen_topography{$_} for @specimens;
} # p @snomed;
# legacy biopsy site that doesn't match anatomical_sites.site_name:
return { code => 'C80.9' } unless @snomed; # site unknown
return scalar @snomed == 1
? { code => $snomed[0] }
: [ map { code => $_ }, @snomed ];
}
# for non-histology specimens (sample_code NOT RLIKE '[DGLRX]([BS]L|F|U)'):
# NB these are ICDO3 topography codes for site of tumour origin
my %specimen_topography = (
BMA => 'C42.1',
BMAT => 'C42.1',
CF => '',
CHIA => 'C42.0', # should never issue new diagnosis on CHIA
CHIB => 'C42.0', # should never issue new diagnosis on CHIB
CHIM => 'C42.0', # should never issue new diagnosis on CHIM
CMP => '', # should never issue new diagnosis on CMP
EF => '',
# HS => '', # require biopsy_site now
# LA => 'C77.9', # require biopsy_site now
PB => 'C42.0',
SE => '', # never issue new diagnosis on SE
TBL => 'C42.1',
TBP => 'C42.1',
TSL => 'C42.1',
URI => '', # never issue new diagnosis on URI
# XA => '', # require biopsy_site now
RXPB => 'C42.0', # should never issue new diagnosis on RXPB
TSM => '', # never issue new diagnosis on TSM
);
=cut
