#!/usr/bin/env perl
=begin -------------------------------------------------------------------------
NGIS data extraction to csv
usage: perl $0 [-tq]
* --query|q = output query to stdout
* --test|t = saves file locally, doesn't email
* --database|d = database
* --reqId 10 --reqId 100 --reqId 10000, etc
query for WGS where sample extracted in Genetics lab & processed at Illumina
- will need adapting if/when arrangement extended to non-WGS samples
test name = wgs_referral (WGS Germline and Tumour), test_id depends on
phenotype (AML/ALL/plasmacytoid, etc) from flow results summary or WGS
'original diagnosis' test result
********************************************************************************
must have either a flow cytometry result summary (diagnostic/primary sample), or
'Original diagnosis (WGS)' result (Germline sample) available on the same day as
WGS Germline and Tumour test requested, or request is skipped
********************************************************************************
TODO: frequency of cron - assumed hourly
TODO: datetime_processing_complete is doing db query for dna extraction date in
NGIS::get_processing_date - what result does csv file expect ?
=cut
#-------------------------------------------------------------------------------
# email addresses to send csv file:
my @recipients = qw(
leedsth-tr.genomicspecimenreception@nhs.net
leedsth-tr.dna@nhs.net
);
my $query_output = 0; # --query|q - output sql queries to console
my $testing = 0; # --testing|t - saves file locally, doesn't email
my $database = 'hilis4'; # --database|d to override
my @REQUEST_IDS = (); # --request_id 1 --request_id 2, etc
my $log_action = 'dispatched WGS datafile'; # for request_history log
my @TEST_NAMES = qw( wgs_referral ); # tests to trigger data transfer
my @null_fields = qw(); # force fields to null if required (temporary measure)
use Getopt::Long;
GetOptions (
"database|d=s" => \$database, # str
"testing|t" => \$testing, # flag
"query|q" => \$query_output, # flag
"reqId=i" => \@REQUEST_IDS, # int list (optional)
);
use strict;
use warnings;
use feature 'say';
my $JUST_TESTING = $testing || 0;
use lib '/home/raj/perl5/lib/perl5';
use FindBin qw($Bin); # warn $Bin;
use IO::All;
use Text::CSV;
use File::Temp;
use Data::Printer;
use SQL::Abstract::More;
use lib $Bin . '/../../../lib';
use LIMS::Local::ScriptHelpers;
use LIMS::Local::NGIS;
use lib '/home/raj/perl-lib';
use Local::DB;
my $tools = LIMS::Local::ScriptHelpers->new();
$tools->test_only($JUST_TESTING);
my $config = $tools->config();
my $today = $tools->time_now;
my $dbix = Local::DB->dbix({ dbname => $database }); # p $dbix;
$dbix->lc_columns = 0; # preserve mixed case on col names (now standardised)
# get NGIS object:
my $ngis = do {
my %args = (
dbix => $dbix, query_output => $query_output, test_mode => $JUST_TESTING
);
LIMS::Local::NGIS->new(%args);
}; # p $ngis;
$Local::DBIx::Simple::Result::NO_AUTO_DATE_INFLATION = 0; # force iso8601 datetime
#-------------------------------------------------------------------------------
my $filename = sprintf 'YNEGLH_HMDS_%s_dispatch.csv',
$today->strftime('%Y%m%d_%H%M%S'); # warn $filename;
$ngis->set_t0(); # start timer for data processing
# 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 $query = do { # _get_main_query returns false if no request_id's to process
my ($sql, @bind) = _get_main_query(\@REQUEST_IDS); # p $sql; p @bind;
exit unless $sql;
$dbix->query( $sql, @bind );
};
# get cols from query, except 'private' ones used for evaluations (eg _datetime_screened):
my @headers = grep $_ !~ /^_/, $query->columns; # p @headers;
# retrieve data from query:
my $data = $query->hashes; $ngis->runtimer('query runtime'); # p $data;
my $content; # container for csv output (live mode; bypassed in test mode)
# pre-process data to reconstitute (some) molecular panels and split (some)
# FISH panels, stores data inside $ngis object:
$ngis->preprocess_data($data);
# store col_headers & null_fields in ngis object for use in process_data():
$ngis->col_headers(\@headers);
$ngis->null_fields(\@null_fields);
# type of filehandle depends on live or test-mode:
my $fh = _get_filehandle();
my $csv = Text::CSV->new ({ binary => 1, auto_diag => 1, eol => $/ });
$csv->print($fh, \@headers);
# retrieve pre-processed data from $ngis:
my @ngis_data = @{$ngis->data}; # p @ngis_data; # AoH
for my $ref (@ngis_data) { # p $ref;
my $row = process_data($ref); # p $row; # arrayref
$csv->print($fh, $row);
}
# need to close $fh before $content becomes available (or it truncates at 1024
# chars; not necessary for test_mode because file persists after end of script):
close $fh or die $!;
$ngis->runtimer('completed data processing');
if ($JUST_TESTING) {
say 'data saved to ' . $fh->filename; # $fh = File::Temp object
}
else { # transfer file by email:
my %mail = (
attachment => $content, # populated via $fh in live mode
filename => $filename,
subject => $filename,
config => $config,
); # p %mail; exit;
$tools->send_mail(\%mail, \@recipients);
{ # have to assume email success, log action to stop subsequent dispatches:
my $service_user = $tools->get_server_user_details();
for my $req (@ngis_data) { # p $req;
my %h = (
request_id => $req->{internal_request_id},
user_id => $service_user->{id},
action => $log_action,
); # p %h;
$dbix->insert('request_history', \%h);
}
}
}
#===============================================================================
sub process_data {
my $ref = shift; # p $ref; # href
# DoB datetime to date:
if ( my $dob = $ref->{patient_dob} ) {
$ref->{patient_dob} = $dob->ymd;
}
$ref->{expected_sample_number} = 2; # always tumour + germline samples
$ref->{order_submitted} = 0; # will be submitted elsewhere
# primary sample; 0 = germline sample, 1 = diagnostic sample:
# TODO: or could use sample_type_dispatched if opts not shared with diagnostic sample
$ref->{primary_sample} = $ref->{_specimen_type} =~ /germline/ ? 0 : 1;
# assume received & dispatched are the same, avoid 2 identical query lookups:
$ref->{sample_type_received} = $ref->{sample_type_dispatched};
# NGIS code for WGS (based on flow phenotype - AML/ALL):
$ref->{test_id} = _get_ngis_code($ref);
# replicating HMDS lab number as external sample ID:
$ref->{external_sample_id} = $ref->{local_sample_id};
$ref->{sample_date_sent} = $today->ymd; # assumes daily procedure
# determine date lab-test requested (replaced by datetime_order_received):
# $ref->{datetime_test_requested} = get_test_request_date($ref); # will need to be revived
my $data = $ngis->finalise_data($ref); # p $data; # adds some new fields, sets others undef
return $data;
}
#-------------------------------------------------------------------------------
sub _get_ngis_code { # regex on results_summary or original_diagnosis value:
my $data = shift; # p $data;
# germline samples use _original_diagnosis, others use _results_summary:
my $phenotype = $data->{_results_summary} || $data->{_original_diagnosis}; # p $phenotype;
return undef if ! $phenotype; # query should prevent this but jic
if ( $phenotype =~ /acute myeloid/ ) {
return 'M80.1';
}
elsif ( $phenotype =~ /acute lymphoblastic/i ) {
return 'M91.1';
}
elsif ( $phenotype =~ /blastic plasmacytoid/i ) {
return 'M90.1';
}
elsif ( $phenotype =~ /myelomonocytic/i ) {
return 'M88.2';
}
elsif ( $phenotype =~ /acute leukaemia/i ) { # other AL
return 'M89.1';
}
else { # TODO: need to improve this - NGIS code is mandatory
warn "no NGIS code for $data->{local_sample_id}";
return undef;
}
}
#-------------------------------------------------------------------------------
sub _get_main_query { # p $_[0]; # optional aref of request_id's
# get request_id's from command-line, or from _get_requests() query, or
# return undef (triggers script exit):
my $request_ids = shift;
unless (@$request_ids) {
my ($sql, @bind) = _get_requests(); # p $sql; p @bind;
$request_ids = $dbix->query( $sql, @bind )->column; # p $request_ids ;
};
return undef if ! @$request_ids; # p $request_ids; exit;
my $cols = _main_query_cols(); # these keep changing
my @rels = ( 'requests|r' ,
q{r.patient_case_id=pc.id} => 'patient_case|pc' ,
q{pc.patient_id=p.id} => 'patients|p' ,
q{pc.referral_source_id=rs.id} => 'referral_sources|rs' ,
q{r.referrer_department_id=rd.id} => 'referrer_department|rd' ,
q{rd.hospital_department_code=hd.id} => 'hospital_departments|hd' ,
q{rd.referrer_id=ref.id} => 'referrers|ref' ,
q{ts.request_id=r.id} => 'request_lab_test_status|ts' ,
q{ts.lab_test_id=lt.id} => 'lab_tests|lt' ,
q{lt.lab_section_id=ls1.id} => 'lab_sections|ls1' ,
q{tr.request_id=r.id} => 'request_lab_test_results|tr' ,
q{tr.lab_test_id=lt2.id} => 'lab_tests|lt2' ,
q{rsp.request_id=r.id} => 'request_specimen|rsp' ,
q{rsp.specimen_id=s.id} => 'specimens|s' ,
# left joins:
q{=>rrs.request_id=r.id} => 'request_result_summaries|rrs' ,
q{=>rrs.lab_section_id=ls2.id} => 'lab_sections|ls2' ,
q{=>pd.patient_id=p.id} => 'patient_demographics|pd' ,
q{=>rst.request_id=r.id} => 'request_storage|rst' ,
q{=>rst.rack_id=sr.id} => 'storage_racks|sr' ,
q{=>rer.request_id=r.id} => 'request_external_ref|rer' ,
q{=>ro.request_id=r.id} => 'request_option|ro' ,
q{=>ro.option_id=ao.id} => 'additional_options|ao' ,
# will not be available if request not reported when file generated:
q{=>rrv.request_id=r.id} => 'request_report_view|rrv' ,
q{=>rsd.request_id=r.id} => 'request_specimen_detail|rsd' ,
);
my %where = (
'ls1.section_name' => 'Whole genome sequencing',
'lt.test_name' => { -in => \@TEST_NAMES },
'r.id' => { -in => $request_ids },
'-or' => [
{ # section_name = 'Flow cytometry' AND flow results summary exists
'ls2.section_name' => 'Flow cytometry',
'rrs.results_summary' => { '!=' => undef },
},
{ # sample_code = 'WGS' AND original_diagnosis result exists
's.sample_code' => 'WGS',
'tr.result' => => { '!=' => undef },
},
],
);
my @args = (
-columns => $cols,
-from => [ -join => @rels ],
-where => \%where,
-group_by => 'r.id', # for group_concat on specimen
-order_by => 'r.id',
# -limit => 5,
# -offset => 350,
); # p @args;
my ($sql, @bind) = $sqla->select(@args); # p $sql; p \@bind;
$dbix->dump_query($sql, @bind) if $query_output; # exit;
return ($sql, @bind);
}
#-------------------------------------------------------------------------------
sub _get_requests {
# query is for test_name = wgs_referral & csv not already dispatched
my $cols = 'DISTINCT(r.id)'; # multiple rh entries (screened, reported, etc)
my @rels = ( 'requests|r' ,
q{ts.request_id=r.id} => 'request_lab_test_status|ts' ,
q{ts.lab_test_id=lt.id} => 'lab_tests|lt' ,
# left joins:
q{=>rh.request_id=r.id} => 'request_history|rh' ,
);
my %where = (
'lt.test_name' => { -in => \@TEST_NAMES },
#'DATE(ts.time)' => $today->ymd,
-or => [
'rh.action' => undef, # required if no rh entry
'rh.action' => { -not_rlike => $log_action },
],
);
my @args = (
-columns => $cols,
-from => [ -join => @rels ],
-where => \%where,
); # p @args;
my ($sql, @bind) = $sqla->select(@args); # p $sql; p \@bind;
$dbix->dump_query($sql, @bind) if $query_output; # exit;
return ($sql, @bind);
}
#-------------------------------------------------------------------------------
sub _main_query_cols {
my $local_lab_name = $ngis->local_lab_name; # p $local_lab_name;
my @cols = (
'CONCAT_WS("/", r.request_number, r.year - 2000)|local_sample_id',
'NULL|local_sample_id_sub',
'NULL|local_dna_number',
'NULL|local_dna_number_sub',
'p.id|internal_patient_id',
'r.id|internal_request_id',
qq!"$local_lab_name"|booking_laboratory!,
qq!"YNEGLH Leeds Shire"|processing_laboratory!, # for WGS
qq!"Illumina"|testing_laboratory!, # for WGS
'NULL|ped_number',
'p.first_name|patient_first_name',
'p.last_name|patient_last_name',
'p.dob|patient_dob',
'p.gender|patient_sex',
'p.nhs_number',
'pd.address|patient_address',
'NULL|patient_district_of_residence',
'NULL|patient_county',
'NULL|patient_city',
'pd.post_code|patient_postcode',
'NULL|patient_country',
'ref.national_code|referrer_unique_code',
'NULL|referrer_email',
'NULL|referrer_telephone',
'NULL|referrer_title',
q!SUBSTRING_INDEX(ref.name, ' ', -1)|referrer_first_name!,
q!LEFT(ref.name, CHAR_LENGTH(ref.name) - LOCATE(' ', REVERSE(ref.name)))
AS referrer_last_name!,
'hd.display_name|referrer_specialty', # required spelling !!
'rs.display_name|referring_facility_name',
'NULL|referrer_address',
'NULL|referrer_city',
'NULL|referrer_district',
'NULL|referrer_county',
'NULL|referrer_postcode',
'NULL|referrer_country',
'rs.organisation_code|referring_facility_ods_code',
'NULLIF( pc.unit_number, "UNKNOWN")|unit_number', # NULL if a = b
'NULL|other_unit_number',
'IFNULL(rrv.clinical_details, "DiagnosticTest")|referral_reason', # a or b
q!"Routine"|test_priority!,
'NULL|test_id', # NGIS test id, will depend on diagnosis (AML vs ALL)
'lt.field_label|test_name', # needs to match test directory
'NULL|ngis_id', # NGIS order number
'NULL|external_sample_id', # rer.external_reference - using HMDS lab-num now
'NULL|external_patient_id',
'NULL|sample_type_received', # set later, same as sample_type_dispatched
'rsd.specimen_date|datetime_sample_collected', # datetime
'r.created_at|datetime_sample_received', # datetime
'r.created_at|datetime_order_received', # datetime
'NULL|datetime_processing_complete', # set later
'rsd.specimen_quality|sample_condition', # not available at upload
q!MAX( CASE WHEN ao.option_name = 'doi'
THEN 'yes' ELSE 'no' END ) AS infection_risk!,
'NULL|sample_transfer_request_comments',
q!MAX( CASE WHEN lt2.test_name = 'sample_type' THEN tr.result END )
AS sample_type_dispatched!,
# WGS samples are whole (BM or PB) so will never have DNA vol, conc, etc
'IF( rst.volume, "ul", NULL )|sample_units',
'rst.volume|sample_amount',
q!IF( rst.concentration < 9999, rst.concentration, NULL )
AS dna_concentration!,
'NULL|sample_date_sent',
'rst.vialId|sample_tube_id',
'sr.plateId|sample_rack_id',
'NULL|sample_courier',
'NULL|sample_courier_ref',
'NULL|expected_sample_number',
'NULL|order_submitted',
'NULL|primary_sample',
# fields used for data processing only (underscored for omission in @headers):
'lt.test_name|_test_name',
'ls1.section_name|_section_name', # WGS
'rrs.results_summary|_results_summary',
# to test for germline sample, superfluous if using sample_type_dispatched:
'GROUP_CONCAT(DISTINCT(s.description))|_specimen_type',
q!MAX( CASE WHEN lt2.test_name = 'original_diagnosis' THEN tr.result
END ) AS _original_diagnosis!,
);
return wantarray ? @cols : \@cols;
}
#-------------------------------------------------------------------------------
sub _get_filehandle {
my $fh;
if ($JUST_TESTING) { # create a temp file:
$fh = File::Temp->new(SUFFIX => '.csv'); # create new fh to tmpfile in /tmp dir
$fh->unlink_on_destroy(0);
}
else { # open filehandle to a reference to a variable:
open $fh, ">:encoding(utf8)", \$content or die $!;
}
return $fh;
}
