#!/usr/bin/env perl
=begin -------------------------------------------------------------------------
requests requiring confirmation of diagnosis (see .local/diagnosis_confirm.yml):
1) request is authorised
2) has no outstanding tests
3) request.status <> 'complete'
4) has a cytogenetics, molecular or FISH results summary timestamp AFTER auth date
screening terms with/without sample types and clinical trials which are exempt
from requiring diagnosis confirmation are defined in diagnosis_confirm.yml
Also sets request status to complete if status = authorised, has no outstanding
tests and NOT in incomplete_requests list ie requiring diagnosis confirmation
#---------------------------------------------------------------------------
# TODO: write .t then move to Local::DB & retest
=cut
use Getopt::Std;
getopts('t'); # testing
our($opt_t);
use strict;
use warnings;
use feature 'say';
my $JUST_TESTING = $opt_t || 0; # dumps HTML file to $Bin/incomplete.html; no emails or db update
#-------------------------------------------------------------------------------
my @recipients = qw( hmds.secure ); # raj sinclair douglas bagguley oconnor
#-------------------------------------------------------------------------------
use lib qw(
/home/raj/perl5/lib/perl5
/home/raj/perl-lib
);
use IO::All;
use Data::Printer;
use SQL::Abstract::More;
use FindBin qw($Bin); # warn $Bin;
use lib "$Bin/../../../lib";
use LIMS::Local::ScriptHelpers;
use Local::DB; # using date auto-inflation
# get tools from LIMS::Local::ScriptHelpers:
my $tools = LIMS::Local::ScriptHelpers->new();
$tools->test_only($JUST_TESTING);
my $config = $tools->config();
my $yaml = $tools->get_yaml_file('diagnosis_confirm'); # p $yaml; exit;
my $dbix = Local::DB->dbix({dbname => 'hilis4'}); # only in use by Leeds
my $sqla = SQL::Abstract::More->new;
my $excluded_screens = $yaml->{exempt_all_sample_types}; # p $excluded_screens;
my $excluded_trials = $yaml->{exempt_clinical_trials}; # p excluded_trials;
# lab sections requiring confirmation of diagnosis:
my $lab_sections = $yaml->{lab_sections}; # p $lab_sections;
my $template = 'cron/incomplete_requests.tt';
my $dump_file = "$Bin/incomplete.html"; # for use if JUST_TESTING
# reset dump_file:
io($dump_file)->unlink if -e $dump_file;
# get list of request_ids where request authorised, status incomplete and have
# molecular, cytogenetic or FISH result summary:
my $request_ids = _get_request_ids(); # p scalar @$request_ids; # arrayref
# globals:
my (
%h, # reporter => request data
%all_lab_tests, # request.id => test_name & status
@requires_confirmation, # request id's requiring confirmation
);
REQUEST:
for my $id (@$request_ids) { # p $id; next unless $id == 241124;
# data for determining whether diagnosis confirmation is required:
my $args = {
specimen => [], # array(ref) of sample_codes
lab_test => [], # AoH (keys = test_name & status)
section => [], # array(ref) of lab_section names
screen => undef, # str
trial => undef, # str (optional)
yaml => $yaml,
};
# get clinical trial:
$args->{trial} = _get_clinical_trial($id); # p $args;
# get initial_screen:
$args->{screen} = _get_initial_screen($id); # p $args;
# get specimen(s) array(ref):
$args->{specimen} = _get_specimen_code($id);
# get lab_tests (AoH):
$args->{lab_test} = _get_lab_tests($id);
# get results_summary section names => result_summary timestamp (AoH):
$args->{section} = _get_rs_section_datetime($id);
# get report data:
my $req = _get_request_report($id);
# add authorisation date for comparison to result summary date:
$args->{authorisation_date} = $req->{auth_date};
# next request if diagnosis confirmation NOT required:
next REQUEST unless $tools->diagnosis_confirmation_required($args);
my $reporter = $req->{report_by}; # p $reporter; next REQUEST;
push @{ $h{$reporter} }, $req;
next REQUEST if $JUST_TESTING; # don't want to update db
# add to @requires_confirmation for use in _get_authorised_requests() query:
push @requires_confirmation, $id; # ie diagnosis confirmation IS required
} # p %h; p @requires_confirmation;
my %mail = ( config => $config, content => 'html' );
# email messages:
REPORTER:
while ( my($reporter, $d) = each %h ) {
my %tt_params = ( reporter => $reporter, data => $d );
my $msg = $tools->process_template($template, \%tt_params);
### uncomment next line to dump to file and NOT send email:
# $msg >> io("$Bin/incomplete.html"); next REPORTER; die;
$mail{message} = $msg; # p $msg; next REPORTER;
$mail{subject} =
sprintf 'HILIS records requiring confirmation of diagnosis on %s [%s]',
$tools->time_now->dmy, uc $reporter;
$JUST_TESTING # dump to file only if just testing
? $msg > io("/tmp/${reporter}_incomplete.html")
: $tools->send_mail(\%mail, \@recipients);
}
set_request_status() unless $JUST_TESTING; # don't want to update db
#===============================================================================
sub set_request_status { # warn 'here'; # die;
# status_option.id of 'complete' requests:
my $status_option_id = _complete_status_option_id();
# server username:
my $server_user = $tools->get_server_user_details(); # p $server_user;
# get list of requests where status = authorised and don't require diagnosis
# confirmation (using @requires_confirmation array to supply list of requests
# where confirmation IS required):
my $authorised_requests = _get_authorised_requests(); # p $authorised_requests;
DATA: # skip any requests with outstanding tests - set rest to status = complete:
for my $data( @$authorised_requests ) { # p $data;
my $lab_test = _get_lab_tests($data->{id}); # p $lab_test;
my @status = map $_->{status}, @$lab_test; # p @status;
next DATA if grep $_ ne 'complete', @status; # skip if ANY test status NOT complete
# warn 'here';
{ # now have authorised case with no outstanding lab-tests and not requiring a
# diagnosis confirmation, so set request status to 'complete':
my %h = (
status_option_id => $status_option_id,
# preserve timestamp to avoid triggering unnecessary report:
updated_at => $data->{updated_at},
); # p %h;
$dbix->update( 'requests', \%h, { id => $data->{id} } );
}
{ # log action in request_history:
my %data = (
request_id => $data->{id},
user_id => $server_user->{id},
action => 'set request status to complete',
); # p %data;
$dbix->insert('request_history', \%data);
}
}
}
# queries ======================================================================
sub _get_request_ids {
my @cols = qw( r.id );
my @rels = (
'requests|r' => 'ris.request_id=r.id' ,
'request_initial_screen|ris' => 'ris.screen_id=s.id' ,
'screens|s' => 'rrs.request_id=r.id' ,
'request_result_summaries|rrs' => 'rrs.lab_section_id=ls.id' ,
'lab_sections|ls' => 'rrd.request_id=r.id' ,
'request_report_detail|rrd' => 'rrd.diagnosis_id=d.id' ,
'diagnoses|d' => '=>rt.request_id=r.id' ,
'request_trial|rt' => '=>rt.trial_id=ct.id' ,
'clinical_trials|ct' => 'r.status_option_id=so.id' ,
'status_options|so'
);
my %where = (
-and => [
's.description' => { -not_in => $excluded_screens },
-or => [
'ct.trial_name' => { -not_in => $excluded_trials },
'ct.trial_name' => undef,
],
-or => [
{
'so.description' => 'authorised',
'ls.section_name' => { -in => $lab_sections },
},
{
'so.description' => 'complete',
'd.name' => {
-rlike => 'awaiting final (diagnosis|review)'
},
},
],
],
);
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
-group_by => 'r.id',
-order_by => [ 'r.year', 'r.request_number' ],
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); # exit;
my $request_ids = $dbix->query($sql, @bind)->column; # p $request_ids;
return $request_ids;
}
sub _get_authorised_requests {
my @cols = qw( r.id r.updated_at );
my @rels = qw( requests|r r.status_option_id=so.id status_options|so );
my %where = (
'so.description' => 'authorised',
'r.id' => { -not_in => \@requires_confirmation }, # global var
);
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $requests = $dbix->query($sql, @bind)->hashes; # p $requests;
return $requests;
}
sub _get_request_report {
my $request_id = shift;
my @cols = (
'r.request_number', 'r.year', 'd.name|diagnosis',
'MAX(CASE WHEN rs.action = "reported" THEN rs.username END)|report_by',
'MAX(CASE WHEN rs.action = "reported" THEN rs.time END)|report_date',
'MAX(CASE WHEN rs.action = "authorised" THEN rs.username END)|auth_by',
'MAX(CASE WHEN rs.action = "authorised" THEN rs.time END)|auth_date',
);
my @rels = (
'requests|r' => 'rs.request_id=r.id',
'request_status_view|rs' => 'rr.request_id=r.id',
'request_report_view|rr' => 'rr.diagnosis_id = d.id',
'diagnoses|d'
);
my %where = ( 'r.id' => $request_id );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $ref = $dbix->query($sql, @bind)->hash; # p $ref;
return $ref;
}
sub _get_clinical_trial {
my $request_id = shift;
my @cols = qw( ct.trial_name );
my @rels = qw( request_trial|rt rt.trial_id=ct.id clinical_trials|ct );
my %where = ( 'rt.request_id' => $request_id );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $val = $dbix->query($sql, @bind)->value; # p $val;
return $val;
}
sub _get_initial_screen {
my $request_id = shift;
my @cols = qw( s.description );
my @rels = qw( request_initial_screen|ris ris.screen_id=s.id screens|s );
my %where = ( 'ris.request_id' => $request_id );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $val = $dbix->query($sql, @bind)->value; # p $val;
return $val;
}
sub _get_specimen_code {
my $request_id = shift;
my @cols = qw( s.sample_code );
my @rels = qw( request_specimen|rs rs.specimen_id=s.id specimens|s );
my %where = ( 'rs.request_id' => $request_id );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $ref = $dbix->query($sql, @bind)->column; # p $ref;
return $ref;
}
sub _get_lab_tests {
my $request_id = shift; # p $request_id;
# function called twice, from REQUEST block & again from set_request_status()
# say "returning $request_id" if $all_lab_tests{$request_id};
return $all_lab_tests{$request_id} if $all_lab_tests{$request_id};
my @cols = qw( lt.test_name so.description|status );
my @rels = (
'request_lab_test_status|ts' => 'ts.status_option_id=so.id' ,
'lab_test_status_options|so' => 'ts.lab_test_id=lt.id' ,
'lab_tests lt'
);
my %where = ( 'ts.request_id' => $request_id );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $ref = $dbix->query($sql, @bind)->hashes; # p $ref;
$all_lab_tests{$request_id} = $ref; # in case requested later
return $ref;
}
sub _get_rs_section_datetime {
my $request_id = shift;
my @cols = qw( ls.section_name rrs.time );
my @rels = qw(
request_result_summaries|rrs rrs.lab_section_id=ls.id lab_sections|ls
);
my %where = ( 'rrs.request_id' => $request_id );
my @args = (
-columns => \@cols,
-from => [ -join => @rels ],
-where => \%where,
);
my ($sql, @bind) = $sqla->select(@args); # p $sql; # p \@bind;
# $dbix->dump_query($sql, @bind); exit;
my $ref = $dbix->query($sql, @bind)->hashes; # p $ref;
return $ref;
}
sub _complete_status_option_id {
$dbix->select('status_options', 'id',
{ description => 'complete' })->into(my $id); # p $id;
return $id;
}
