#!/usr/bin/env perl
=begin -------------------------------------------------------------------------
NGIS data extraction; check ngis_* tables up-to-date
runs at 6am on 1st & 3rd Friday of month via cron:
0 6 1-7 * * [ "$(date '+\%a')" = "Fri" ] && $MULTI/$0 ...
0 6 15-21 * * [ "$(date '+\%a')" = "Fri" ] && $MULTI/$0 ...
manual run: $0 options:
-m = months
-t = testing: saves files locally, doesn't email
-q = query output
--cumulative = all requests since 1st of month of ref date
--console = verbose log to console
--verbose = verbose log to file (overrides console)
--reqId 10 --reqId 100 --reqId 10000, etc
maps hilis4 lab tests to an NGIS test code using hilis4.ngis_lab_test table:
if lab_test_id entry(s) exist in ngis_lab_test table:
* if single row then use ngis_test_code value (diagnosis doesn't matter so request
doesn't need to be reported)
* if lab_test has multiple ngis_test_codes, the diagnosis clinical indication code
(ngis_diagnosis.ngis_indication_id) is used to determine which (if any)
ngis_test_code to use, where the diagnosis clinical indication must match
one of the available ngis test id's eg HTS myeloid test has matching codes
for a diagnosis of MDS, MPN, etc but not for CML
* if NGIS test code cannot be found on diagnosis, a loose matching on presentation
is attempted, including previous screen terms used, eg 'MDS' matches
'Suspected MDS', 'Follow-up MDS'
* last resort is to force NGIS test code onto some test names (eg HTS myeloid)
* recipient does not want technology (FISH, PCR, HTS, etc) so ETV6/RUNX1 (FISH)
& ETV6-RUNX1 (PCR) potentially ambiguous
* molecular tests are reassembled into panels (if panel has NGIS code)
* FISH panels without NGIS codes are expanded to individual tests
TODO: for molecular panels when 1 or more tests set complete in different months,
panel not recognised and separate test codes returned eg 20536/19
complications (see geneq_data_extract.log):
* hilis4 lab-tests/panels without ngis test id's - require default codes
* lab tests/panels without a clinical indication mapped to diagnosis or screen
* diagnostic terms without clinical indication (eg 'see comments', 'lab tests only', etc)
* requests not reported when data collected
=cut
#-------------------------------------------------------------------------------
#===============================================================================
my @data_recipients = qw( paul.mcintosh john.fraser raj );
my @log_recipients = qw( turner talley raj );
#===============================================================================
# new template wants some cols temporarily NULL (commented out in query now):
my @null_fields = qw//;
my $query_output = 0; # --query|q - output sql queries to console
my $log_console = 0; # --console - verbose log to console
my $verbose_log = 0; # --verbose - verbose log to file (overrides --console)
my $cumulative = 0; # --cumulative - all requests since 1st of month of ref_date
my $duration = 1; # --month|m - default unless specified in command-line opts
my $testing = 0; # --testing|t - saves file locally, doesn't email
my @REQUEST_IDS = (); # --request_id 1 --request_id 2, etc
use Getopt::Long;
GetOptions (
"months|m=i" => \$duration, # int
"testing|t" => \$testing, # flag
"query|q" => \$query_output, # flag
"console" => \$log_console, # flag
"verbose" => \$verbose_log, # flag
"cumulative" => \$cumulative, # flag
"reqId=i" => \@REQUEST_IDS, # int list (optional)
); # warn $duration; warn $cumulative; exit;
use strict;
use warnings;
my $JUST_TESTING = $testing || 0;
use lib '/home/raj/perl5/lib/perl5';
use FindBin qw($Bin); # warn $Bin;
use Data::Printer;
use Log::Any qw($log);
use Log::Any::Adapter;
use SQL::Abstract::More;
use List::Util qw(maxstr);
use Spreadsheet::WriteExcel::Simple;
use lib $Bin . '/../../../lib';
use LIMS::Local::ScriptHelpers;
use LIMS::Local::NGIS;
use lib '/home/raj/perl-lib';
use Local::WriteExcel;
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 => 'hilis4' });
$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 = 1; # or will defeat DATE(col)
#-------------------------------------------------------------------------------
my $ref_date = $today->clone->subtract( months => $duration ); # warn $ref_date;
my $filename = sprintf 'GeNEQ_HMDS_data_%s.xls', $ref_date->strftime('%b_%Y'); # warn $filename;
my $subject = sprintf 'GeNEQ HMDS data %s', $ref_date->strftime('%b %Y');
my $logfile = sprintf '%s/geneq_data_extract_%s.log',
$Bin . '/../../../logs/geneq', lc $ref_date->strftime('%b_%Y'); # warn $logfile;
# for verbose logging to console (can be set or reset later):
Log::Any::Adapter->set('Stdout') if $log_console;
# for verbose logging to logfile (can be set or reset later):
Log::Any::Adapter->set(File => $logfile) if $verbose_log;
$ngis->set_t0(); # start timer for data processing
my $query = do {
my ($sql, @bind) = _get_main_query(); # p $sql; p @bind;
$dbix->query( $sql, @bind );
};
{ # retrieve data from query and populate $ngis->data:
my $data = $query->hashes; $ngis->runtimer('query runtime'); # p $data; exit;
# pre-process data to reconstitute (some) molecular panels and split (some)
# FISH panels, stores data inside $ngis object:
$ngis->preprocess_data($data);
}
my $xl = Spreadsheet::WriteExcel::Simple->new;
my @headers = grep $_ !~ /^_/, $query->columns; # p @headers;
$xl->write_bold_row(\@headers);
# store in ngis object for data generation:
$ngis->col_headers(\@headers);
$ngis->null_fields(\@null_fields);
# retrieve preprocessed data from $ngis:
my @data = @{$ngis->data}; # p @data; # AoH
for my $ref (@data) { # p $ref;
my $row = process_data($ref); # returns arrayref
$xl->write_row($row);
}
$ngis->runtimer('completed data processing');
if ($JUST_TESTING) {
$xl->save(join '/', $Bin, $filename);
}
else {
my %mail = (
attachment => $xl->data,
filename => $filename,
subject => $subject,
config => $config,
);
$tools->send_mail(\%mail, \@data_recipients);
}
# log all misfits:
_do_log();
#===============================================================================
sub process_data {
my $ref = shift; # p $ref; # href
# determine date lab-test requested (replaced by datetime_order_received):
# $ref->{datetime_test_requested} = get_test_request_date($ref); # will need to be revived
# set datetime_testing_complete to test completion datetime:
$ref->{datetime_testing_complete} = $ref->{_datetime_test_completed};
{ # set datetime_reporting_complete to later of testing_complete or authorisation:
if ( $ref->{_datetime_authorised} ) {
my @dates = @{$ref}{ qw/_datetime_authorised _datetime_test_completed/ };
# dates in yyyy-mm-dd format can be handled as strings for determination
# of chronology using List::Util::maxstr or could do $dateA gt $dateB:
$ref->{datetime_reporting_complete} = maxstr(@dates); # List::Util
}
else { # not authorised, set to _datetime_test_completed:
$ref->{datetime_reporting_complete} = $ref->{_datetime_test_completed}
}
}
=begin # datetime_processing_complete now set to D/RNA extraction date
# set datetime_processing_complete to later of authorisation date or test
# completion date; value will be null if request not yet authorised:
# p $ref->{sample_processed_date}; p $ref->{_datetime_authorised};
if ( $ref->{_datetime_authorised} ) {
my @dates = @{$ref}{ qw/_datetime_authorised datetime_testing_complete/ };
# dates in yyyy-mm-dd format can be handled as strings for determination
# of chronology using List::Util::maxstr or could do $dateA gt $dateB:
$ref->{datetime_processing_complete} = maxstr(@dates); # List::Util
} # else sample_completed_date remains null
=cut
my $data = $ngis->finalise_data($ref); # adds some new fields, sets others undef
return $data;
}
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!"$local_lab_name"|processing_laboratory!,
qq!"$local_lab_name"|testing_laboratory!,
qq!"$local_lab_name"|reporting_laboratory!,
# '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_city',
# 'pd.post_code|patient_postcode',
# 'NULL|patient_country',
'ref.national_code|referrer_ods_code',
# 'NULL|referrer_email',
# 'NULL|referrer_telephone',
# 'NULL|referrer_title',
# 'NULL|referrer_first_name',
# 'ref.name|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_postcode',
# 'NULL|referrer_county',
'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 (eg M80.6)
'lt.field_label|test_name',
# 'ls.section_name|lab_section',
'NULL|ngis_id', # NGIS order number ?
# 'NULL|datetime_test_requested', # replaced by datetime_order_received
# 'lt.test_type|request_comments', # panel or test
q!GROUP_CONCAT(DISTINCT s.description SEPARATOR '; ')
AS sample_type_received!,
'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
'NULL|datetime_testing_complete', # set later
'NULL|datetime_reporting_complete', # set later
'rsd.specimen_quality|sample_condition',
# q!MAX( CASE WHEN ao.option_name = 'doi'
# THEN 'yes' ELSE 'no' END ) AS infection_risk!,
# 'NULL|sample_type_dispatched',
# '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|sample_processed_date', # renamed datetime_processing_complete
# 'NULL|sample_completed_date', # renamed datetime_testing_complete
# fields used for data processing only (underscored for omission in @headers):
'lt.id|_lab_test_id',
'lt.test_type|_test_type',
'lt.test_name|_test_name',
'ls.section_name|_section_name',
'd.name|_diagnosis',
'nci.code|_clinical_indication_code',
's2.description|_presentation',
'rrv.diagnosis_id|_diagnosis_id',
# q!MAX( CASE WHEN rsv.action = 'screened' THEN rsv.time END )
# AS _datetime_screened!, # not used
# q!MAX( CASE WHEN rsv.action = 'reported' THEN rsv.time END )
# AS _datetime_reported!, # not used
q!MAX( CASE WHEN rsv.action = 'authorised' THEN rsv.time END )
AS _datetime_authorised!,
'ts.time|_datetime_test_completed', # date lab-test set to complete
);
return wantarray ? @cols : \@cols;
}
sub _get_main_query {
my $is_private = q!MAX( CASE WHEN ao.option_name = 'private' THEN 1 END )!;
my $begin_date = $ref_date->clone->set_day(1); # first day of $ref_date month
my %date_restriction = $cumulative # if --cumulative Getopt:
? ( '>=', $begin_date->ymd ) # all since ref_date
: ( -between => [ # first & last day of ref_date month:
$begin_date->ymd, # 1st day
$begin_date->add(months => 1)->subtract(days => 1)->ymd, # last day
] );
my $excluded_lab_test_ids = $ngis->excluded_lab_test_ids;
my $excluded_parent_codes = $ngis->excluded_parent_codes;
my $excluded_test_name_re = $ngis->excluded_test_names;
my $lab_sections = $ngis->included_lab_sections;
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{rs.parent_organisation_id=po.id} => 'parent_organisations|po' ,
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{rsd.request_id=r.id} => 'request_specimen_detail|rsd' ,
q{rsp.request_id=r.id} => 'request_specimen|rsp' ,
q{rsp.specimen_id=s.id} => 'specimens|s' ,
q{ts.request_id=r.id} => 'request_lab_test_status|ts' ,
q{ts.status_option_id=so.id} => 'lab_test_status_options|so' ,
q{ts.lab_test_id=lt.id} => 'lab_tests|lt' ,
q{lt.lab_section_id=ls.id} => 'lab_sections|ls' ,
q{rsv.request_id=r.id} => 'request_status_view|rsv' ,
q{ris.request_id=r.id} => 'request_initial_screen|ris' ,
q{ris.screen_id=s2.id} => 'screens|s2' ,
# left joins:
q{=>rrv.request_id=r.id} => 'request_report_view|rrv' ,
q{=>rrv.diagnosis_id=d.id} => 'diagnoses|d' ,
q{=>nd.diagnosis_id=d.id} => 'ngis_diagnosis|nd' ,
q{=>nd.ngis_indication_id=nci.id} => 'ngis_clinical_indications|nci',
q{=>ro.request_id=r.id} => 'request_option|ro' ,
q{=>ro.option_id=ao.id} => 'additional_options|ao' ,
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{=>rt.request_id=r.id} => 'request_trial|rt' ,
);
my @where = ( # contains repeated elements (eg parent_code), so requires array
'rt.request_id' => undef, # not in clinical trial
'so.description' => 'complete', # lab-test status
'ls.section_name' => { -in => $lab_sections },
'rs.organisation_code' => { -not_rlike => '^NT' }, # private hospital
'po.parent_code' => { -not_rlike => '^(S|Z)' }, # scotland/ireland
'po.parent_code' => { -not_in => $excluded_parent_codes },
'lt.test_name' => { -not_rlike => $excluded_test_name_re },
'lt.id' => { -not_in => $excluded_lab_test_ids },
);
# restrict on request id's if supplied, or date:
if (@REQUEST_IDS) {
push @where, ( 'r.id' => { -in => \@REQUEST_IDS } );
}
else {
push @where, ( 'DATE(ts.time)' => \%date_restriction );
} # p @where;
my @args = (
-columns => $cols,
-from => [ -join => @rels ],
# contains repeated elements (eg parent_code), so requires "-and => aref"
-where => { -and => \@where },
-group_by => [ 'lt.id', 'r.id' ],
-having => { $is_private => undef }, # not private patient
-order_by => 'r.id',
#-limit => 100,
#-offset => 100,
); # 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) if $query_output; # exit;
return ($sql, @bind);
}
sub _do_log {
my $stash = $ngis->log_stash; # p $stash;
my $no_ngis_code = $stash->{no_ngis_code};
my $unreported = $stash->{unreported};
my $no_clinical_indication = $stash->{no_clinical_indication};
my $no_available_ngis_code = $stash->{no_available_ngis_code};
my $filename = sprintf '%s/geneq_data_extract_log_%s.xlsx',
$Bin . '/../../../logs/geneq', lc $ref_date->strftime('%b_%Y');
my $xl = Local::WriteExcel->new( filename => $filename ); # p $xl;
if ($no_clinical_indication) {
$xl->worksheet_name('no clinical indication');
my @cols = qw( lab_num test_name presentation diagnosis );
$xl->write_bold_row(\@cols);
$xl->write_row($_) for @$no_clinical_indication;
}
if ($no_available_ngis_code) {
$xl->worksheet_name('no available ngis test-code');
my @cols = qw( lab_num test_name ngis_codes diagnosis
clinical_indication presentation );
$xl->write_bold_row(\@cols);
$xl->write_row($_) for @$no_available_ngis_code;
}
if ($unreported) {
$xl->worksheet_name('unreported');
$xl->write_bold_row([ qw/lab_num test_name presentation/] );
$xl->write_row($_) for @$unreported;
}
if ($no_ngis_code) { # p $no_ngis_code;
$xl->worksheet_name('no ngis test-code');
$xl->write_bold_row([ qw/test_name test_type lab_section count/ ] );
$xl->write_row([ (split ' :: ', $_ ), $no_ngis_code->{$_} ])
for sort keys %{ $no_ngis_code };
}
if ($JUST_TESTING) {
$xl->save();
}
else {
my $subject = 'GeNEQ data extraction log '
. $ref_date->strftime('%b %Y'); # p $subject;
# capture filename from its full path:
$filename =~ /(geneq_data_extract_log_.*)/; # p $1;
my %mail = (
attachment => $xl->data,
filename => $1, # captured from above
subject => $subject,
config => $config,
);
$tools->send_mail(\%mail, \@log_recipients);
}
{ # text file:
# log summary data to $logfile, override any previous adapter settings
Log::Any::Adapter->set(File => $logfile);
if ($no_clinical_indication) {
$log->info('DIAGNOSIS & PRESENTATION WITH NO CLINICAL INDICATION');
$log->info(join ' :: ', @$_)
for sort test_name_order @$no_clinical_indication;
}
if ($no_available_ngis_code) { # p $no_available_ngis_code;
$log->info('DIAGNOSIS WITH NO AVAILABLE NGIS CODE & PRESENTATION '
. 'WITH NO CLINICAL INDICATION');
$log->info(join ' :: ', @$_)
for sort test_name_order @$no_available_ngis_code;
}
if ($unreported) {
$log->info('UNREPORTED REQUESTS');
$log->info(join ' :: ', @$_) for @$unreported;
}
if ($no_ngis_code) {
$log->info('LAB TESTS WITH NO NGIS ID');
$log->info(join ':: ', $_, $no_ngis_code->{$_})
for sort keys %{ $no_ngis_code };
}
}
}
sub test_name_order { # p $a; p $b;
my ($req_num_a, $yr_a) = split '/', $a->[0];
my ($req_num_b, $yr_b) = split '/', $b->[0];
my $test_name_a = $a->[1];
my $test_name_b = $b->[1];
return $test_name_a cmp $test_name_b
|| $yr_a <=> $yr_b || $req_num_a <=> $req_num_b;
}
sub _test_name_order { # p $a; p $b;
my ($req_num_a, $yr_a, $test_name_a) = $a =~ m!^(\d+)/(\d{2})\: (.*) \[!; # p $test_name_a;
my ($req_num_b, $yr_b, $test_name_b) = $b =~ m!^(\d+)/(\d{2})\: (.*) \[!; # p $test_name_b;
return $test_name_a cmp $test_name_b
|| $yr_a <=> $yr_b || $req_num_a <=> $req_num_b;
}
