#!/usr/bin/perl
use Test::WWW::Mechanize::CGIApp;
use Test::Builder::Tester;
use Data::Dumper;
use strict;
use warnings;
use constant TESTS => 76;
use Test::More tests => TESTS;
# use Test::More 'no_plan';
# tests rules for requiring diagnosis confirmation at report stage:
=begin: tests:
all tests performed on a request with a molecular results summary:
1) request with exempt screen (PNH)
2) request with exempt screen if specimen type (CML interferon follow-up) + LU
3) request with exempt screen if specimen type (CML interferon follow-up) + PB
4) request with exempt screen if specimen type & test (CMPD pres & follow-up) + PB + JAK2 + CML
5) request with exempt screen if specimen type & test (CMPD pres & follow-up) + PB + BMAT + JAK2
6) request with exempt screen if specimen type & test (CMPD pres & follow-up) + PB JAK2
=cut
BEGIN {
require 't/test-lib.pl';
}
my $dbh;
eval {
$dbh = get_dbh() or die 'no database handle recieved from get_dbh';
};
warn $@ if $@;
# vars needed if tests are run:
use vars qw($mech $dbix $spell_check_required);
my $yaml;
eval {
my $src = './config/.local/diagnosis_confirm.yml';
$yaml = YAML::Tiny->read($src);
};
if ($yaml) {
$mech = get_mech();
$dbix = get_dbix();
# need to see if 'require_spell_check' is required:
$spell_check_required = is_spell_check_required(); # warn $spell_check_required;
}
SKIP: {
skip('these tests require config/.local/diagnosis_confirm.yml file',TESTS) unless $yaml;
do_all_tests();
}
sub do_all_tests {
do_login();
# register some new data (fresh tissue):
{ # new screen term which requires a final_diagnosis check:
$dbix->insert('screens',
{ description => 'CML interferon follow-up', category_id => 1 }
);
# new screen term which doesn't require a final_diagnosis check (if PB & jak2):
$dbix->insert('screens',
{ description => 'CMPD pres & follow-up', category_id => 1 }
);
$dbix->insert( 'lab_tests',
{ test_name => 'jak2', field_label => 'JAK2', lab_section_id => 3,
test_type => 'test', has_results => 'no' }
);
# new screen terms requests molecular lab_tests:
$dbix->insert('screen_lab_test',
{ screen_id => 3, lab_test_id => 5 } # APML - is a Molecular test
);
$dbix->insert('screen_lab_test',
{ screen_id => 4, lab_test_id => 10 } # JAK2 - is a Molecular test
);
# new user to change reporter so can authorise:
$dbix->insert('users', { username => 'user1' }); # only required field
# change Flow lab_section 'has_test_sign_out' value:
$dbix->update( 'lab_sections',
{ has_test_sign_out => 'yes' }, { section_name => 'Flow' }
);
}
# 1) PNH exempt from final_diagnosis confirmation:
# screen request:
$mech->get_ok('/screen/=/1'); # print_and_exit();
{
_do_screen(2,'PNH'); # print_and_exit();
}
# sign off result:
$mech->get_ok('/result/=/1'); # print_and_exit();
{
_do_results_sign_off('flow_results'); # print_and_exit();
}
# report & authorise record:
$mech->get_ok('/report/=/1'); # print_and_exit();
{
_do_report(1); # print_and_exit();
}
# should be status = complete:
is( _get_status_option(1), 5, 'OK: expected request status found' ); # print_and_exit();
#-------------------------------------------------------------------------------
# 2) CML interferon follow-up on LU sample - requires comfirmation:
# screen request so it can be reported:
$mech->get_ok('/screen/=/2'); # print_and_exit();
{
_do_screen(3,'CML interferon follow-up'); # print_and_exit();
}
# sign off result & enter result summary:
$mech->get_ok('/result/=/2'); # print_and_exit();
{
_do_results_summary(); # print_and_exit();
}
# report record:
$mech->get_ok('/report/=/2'); # print_and_exit();
{
_do_report(2); # print_and_exit();
}
# should NOT be status = complete:
is( _get_status_option(2), 4, 'OK: expected request status found' ); # print_and_exit();
# re-report and check final_diagnosis box:
$mech->get_ok('/report/=/2'); # print_and_exit();
{
_do_re_report(2); # print_and_exit();
}
# should now be status = complete:
is( _get_status_option(2), 5, 'OK: expected request status found' ); # print_and_exit();
#-------------------------------------------------------------------------------
# 3) CML interferon follow-up on PB - exempt from confirmation:
_register_new_request(3);
$mech->get_ok('/screen/=/3'); # print_and_exit();
{
_do_screen(3,'CML interferon follow-up'); # print_and_exit();
}
# sign off result & enter result summary:
$mech->get_ok('/result/=/3'); # print_and_exit();
{
_do_results_summary(); # print_and_exit();
}
# report record:
$mech->get_ok('/report/=/3'); # print_and_exit();
{
_do_report(3); # print_and_exit();
}
# should be status = complete:
is( _get_status_option(3), 5, 'OK: expected request status found' ); # print_and_exit();
#-------------------------------------------------------------------------------
# 4) CMPD pres & follow-up on PB with JAK2 + CML tests - requires confirmation:
_register_new_request(4);
$mech->get_ok('/screen/=/4'); # print_and_exit();
{
_do_screen(4,'CMPD pres & follow-up'); # print_and_exit();
}
# request new lab_test and sign it off:
$mech->get_ok('/result/=/4'); # print_and_exit();
{
$mech->form_name('flow_requests');
$mech->tick('test_id', 2, 1);
$mech->submit(); # print_and_exit();
$mech->get_ok('/result/=/4'); # print_and_exit();
_do_results_sign_off('flow_results'); # print_and_exit();
}
# sign off result & enter result summary:
$mech->get_ok('/result/=/4'); # print_and_exit();
{
_do_results_summary(); # print_and_exit();
}
# report record:
$mech->get_ok('/report/=/4'); # print_and_exit();
{
_do_report(4); # print_and_exit();
}
# should NOT be status = complete:
is( _get_status_option(4), 4, 'OK: expected request status found' ); # print_and_exit();
# re-report and check final_diagnosis box:
$mech->get_ok('/report/=/4'); # print_and_exit();
{
_do_re_report(4); # print_and_exit();
}
# should now be status = complete:
is( _get_status_option(4), 5, 'OK: expected request status found' ); # print_and_exit();
#-------------------------------------------------------------------------------
# 5) CMPD pres & follow-up on PB & BMAT with JAK2 - requires confirmation:
_register_new_request(5, 'pb,bmat');
$mech->get_ok('/screen/=/5'); # print_and_exit();
{
_do_screen(4,'CMPD pres & follow-up'); # print_and_exit();
}
# sign off result & enter result summary:
$mech->get_ok('/result/=/5'); # print_and_exit();
{
_do_results_summary(); # print_and_exit();
# BMAT requests AUTO (histology) test:
$mech->get_ok('/result/=/5'); # print_and_exit();
_do_results_sign_off('histology_results'); # print_and_exit();
}
# report record:
$mech->get_ok('/report/=/5'); # print_and_exit();
{
_do_report(5); # print_and_exit();
}
# should NOT be status = complete:
is( _get_status_option(5), 4, 'OK: expected request status found' ); # print_and_exit();
# re-report and check final_diagnosis box:
$mech->get_ok('/report/=/5'); # print_and_exit();
{
_do_re_report(5); # print_and_exit();
}
# should now be status = complete:
is( _get_status_option(5), 5, 'OK: expected request status found' ); # print_and_exit();
#-------------------------------------------------------------------------------
# 5) CMPD pres & follow-up on PB with JAK2 only - exempt from confirmation:
_register_new_request(6);
$mech->get_ok('/screen/=/6'); # print_and_exit();
{
_do_screen(4,'CMPD pres & follow-up'); # print_and_exit();
}
# sign off result & enter result summary:
$mech->get_ok('/result/=/6'); # print_and_exit();
{
_do_results_summary(); # print_and_exit();
}
# report record:
$mech->get_ok('/report/=/6'); # print_and_exit();
{
_do_report(6); # print_and_exit();
}
# should be status = complete:
is( _get_status_option(6), 5, 'OK: expected request status found' ); # print_and_exit();
}
sub _register_new_request {
my $request_number = shift;
my $specimen = shift || 'pb';
$mech->get_ok('/request/add_new/2'); # print_and_exit();
$mech->submit_form(
fields => {
request_number => $request_number,
referrer_code => 'C9999998',
specimen => $specimen,
}
); # print_and_exit();
}
sub _get_status_option {
my $id = shift;
my $status_option_id = $dbix->query(
q!select status_option_id from requests where id = ?!, $id
)->list;
return $status_option_id;
}
sub _do_screen {
my ($screen_id, $screen) = @_;
$mech->field(screen_id => $screen_id);
$mech->field(option_id => 1);
$mech->submit();
$mech->has_tag_like(
p => qr(Screened as $screen),
'OK: expected screen term found',
);
}
sub _do_results_summary {
my $text = 'molecular result summary';
$mech->form_name('molecular_results');
$mech->field(results_summary => $text);
$mech->tick('complete_all_tests', 1, 1);
$mech->submit();
$mech->has_tag_like(
td => qr($text),
'OK: expected text found',
);
}
sub _do_results_sign_off {
my $form_name = shift;
$mech->form_name($form_name);
$mech->tick('complete_all_tests', 1, 1);
$mech->submit();
}
sub _do_report {
my $id = shift;
my $report = _get_report();
$mech->form_name('reportForm');
$mech->submit_form(fields => $report); # print_and_exit();
$mech->submit_form(form_name => 'reportForm') if $spell_check_required;
my $msg = get_messages('action')->{edit_success};
$mech->has_tag_like(
p => qr($msg),
'OK: record updated successfully',
); # print_and_exit() if $id == 5;
# have to manually change reporter ID or self-auth refused:
$dbix->update(
'request_history',
{ user_id => 2 },
{ request_id => $id, action => 'reported' }
);
# skip pre-auth check:
$mech->get_ok("/report/=/$id?pre-authorisation-check=1"); # print_and_exit();
$mech->form_name('reportForm');
$mech->field( authorise => 1 );
$mech->submit_form(); # print_and_exit();
$mech->submit_form(form_name => 'reportForm') if $spell_check_required;
$mech->has_tag_like(
p => qr($msg),
'OK: record updated successfully',
); # print_and_exit();
$mech->has_tag_like(
p => qr(Authorised by Admin_fname Admin_lname),
'OK: expected authoriser details found',
);
}
sub _do_re_report {
my $id = shift;
$mech->form_name('reportForm');
$mech->tick('final_diagnosis', 1, 1);
$mech->submit_form(); # print_and_exit();
$mech->submit_form(form_name => 'reportForm') if $spell_check_required;
}
sub _get_report {
return {
status => 'default',
clinical_details => 'some details here',
gross_description => 'gross description here',
comment => 'morphology comment here',
specimen_quality => 'adequate',
diagnosis_id => 1,
};
}
