#!/usr/bin/perl
# requires presence of config/.local/auto_reportable.yml file, or skips tests
#========== NEED TO CHANGE SCREENING TERMS TO MATCH YAML FILE ENTRIES ==========
our @screening_terms = (
'Suspected myeloproliferative',
'Follow-up CML (PB)',
);
#===============================================================================
use Test::WWW::Mechanize::CGIApp;
use Data::Dumper;
use strict;
use warnings;
use constant TESTS => 32;
use Test::More tests => TESTS;
# use Test::More 'no_plan';
=begin: tests:
=cut
BEGIN {
require 't/test-lib.pl';
}
my $yaml = get_yaml('auto_reportable'); # warn Dumper $yaml;
SKIP: {
skip('these tests require config/.local/settings/auto_reportable.yml file',TESTS) unless $yaml;
do_all_tests();
}
sub do_all_tests {
my $mech = get_mech();
do_login();
my $dbh;
eval {
$dbh = get_dbh() or die 'no database handle recieved from get_dbh';
};
# register data for auto_authorisation:
my $dbix = get_dbix();
my $result_summary_option = 'sample shows evidence of Val617Phe JAK2 mutation';
# 2 new screening terms (fresh tissue):
for (@screening_terms) {
$dbix->insert('screens', {
description => $_, category_id => 1, active => 'yes',
});
}
$dbix->insert('diagnoses', {
name => 'Consistent with chronic myeloproliferative disorder',
diagnostic_category_id => 1, active => 'yes',
});
$dbix->insert('diagnoses', {
name => 'Awaiting final diagnosis',
diagnostic_category_id => 3, active => 'yes',
});
{ # lab_tests & lab_test_sample_type:
my @test_ids;
$dbix->insert('lab_tests', {
field_label => 'JAK2 V617F', lab_section_id => 3, test_type => 'test',
has_results => 'no', is_active => 'yes', test_name => 'jak2',
}); push @test_ids, get_last_insert_id('lab_tests');
$dbix->insert('lab_tests', {
field_label => 'CML RQ', lab_section_id => 3, test_type => 'test',
has_results => 'no', is_active => 'yes', test_name => 'cml',
}); push @test_ids, get_last_insert_id('lab_tests');
$dbix->insert('lab_tests', {
field_label => 'RNA extraction', lab_section_id => 3, test_type => 'test',
has_results => 'no', is_active => 'yes', test_name => 'rna_extraction',
}); push @test_ids, get_last_insert_id('lab_tests'); # warn Dumper \@test_ids;
my $sample_type_ids = $dbix->select('lab_section_sample_type',
['sample_type_id'], { lab_section_id => 3 } )->flat; # warn Dumper $sample_type_ids;
for my $id (@test_ids) {
$dbix->insert('lab_test_sample_type',
{ lab_test_id => $id, sample_type_id => $_ }) for @$sample_type_ids;
}
}
$dbix->insert('result_summary_options', {
description => $result_summary_option, lab_section_id => 3, is_active => 'yes',
});
$dbix->insert('screen_lab_test', {screen_id => 3, lab_test_id => 10}); # JAK2
$dbix->insert('screen_lab_test', {screen_id => 3, lab_test_id => 12}); # JAK2
$dbix->insert('screen_lab_test', {screen_id => 4, lab_test_id => 11}); # CML
$dbix->insert('screen_lab_test', {screen_id => 4, lab_test_id => 12}); # CML
# register new:
$mech->get_ok('/request/add_new/2');
{
$mech->submit_form(
fields => {
request_number => 3,
specimen => 'PB',
referrer_code => 'C1234567',
},
); # print_and_exit();
$mech->has_tag(
h3 => 'New request successful',
);
}
# screen request with auto-reportable term:
$mech->get_ok('/screen/=/3'); # print_and_exit();
{
$mech->form_name('initialScreen'); # 1st one is patient notes
$mech->field(screen_id => 3);
$mech->field(option_id => 1);
$mech->submit(); # print_and_exit();
$mech->text_contains(
"Screened as $screening_terms[0]", # 1st one
'OK: expected screen term found',
);
} # print_and_exit();
# sign out tests:
$mech->get_ok('/worklist/display/3?display_format=Data+Entry');
{
$mech->tick('request_lab_test_id', $_, 1) for (1,2); # sign off both tests
$mech->field(status_option_id => 2);
$mech->submit(); # print_and_exit();
$mech->has_tag_like(
p => qr(records updated successfully),
'OK: update success',
); # print_and_exit();
for ('JAK2 V617F', 'RNA extraction', 'complete' ) {
$mech->has_tag(td => $_);
}
}
# section result summary should trigger auto-report/authorisation:
$mech->get_ok('/result/=/3'); # print_and_exit();
{
$mech->form_name('molecular_results');
$mech->field( _results_summary => $result_summary_option);
$mech->submit(); # print_and_exit();
$mech->has_tag_like(
p => get_messages('results')->{update_success},
'OK: update success',
); # print_and_exit();
# check 'reported by' & 'authorised by':
$mech->has_tag_like(
p => qr(Reported by),
'OK: reporter information displayed'
);
# can turn 'authorise' flag on & off in config file:
my $is_authorised = $yaml->{$screening_terms[0]}->{authorise};
if ($is_authorised) {
$mech->has_tag_like(
p => qr(Authorised by),
'OK: authoriser information displayed'
); # print_and_exit();
}
else {
$mech->content_lacks(
'Authorised by',
'OK: lacks authoriser information'
);
} # print_and_exit();
}
# register new:
$mech->get_ok('/request/add_new/2');
{
$mech->submit_form(
fields => {
request_number => 4,
specimen => 'PB',
referrer_code => 'C1234567',
},
); # print_and_exit();
$mech->has_tag(
h3 => 'New request successful',
);
}
# screen another request with auto-reportable term:
$mech->get_ok('/screen/=/4'); # print_and_exit();
{
$mech->form_name('initialScreen'); # 1st one is patient notes
$mech->field(screen_id => 4);
$mech->field(option_id => 1);
$mech->submit(); # print_and_exit();
$mech->text_contains(
"Screened as Follow-up CML (PB)",
'OK: expected screen term found',
);
} # print_and_exit();
# section result summary should trigger auto-report/authorisation:
$mech->get_ok('/result/=/4'); # print_and_exit();
{
my $result_summary = "BCR-ABL transcription number = 200\n"
. "ABL transcription number = 20\n"
. "BCR-ABL : ABL ratio = 2%";
$mech->form_name('molecular_results');
$mech->field(results_summary => $result_summary);
$mech->tick('complete_all_tests', 1, 1);
$mech->submit(); # print_and_exit();
$mech->has_tag_like(
p => get_messages('results')->{update_success},
'OK: update success',
); # print_and_exit();
my @terms = ('Awaiting final diagnosis', 'BCR-ABL transcription number',
'See RQ PCR result');
$mech->text_contains(
$_,
"OK: expected entry '$_' present",
) for @terms; # print_and_exit();
# check 'reported by' & 'authorised by':
$mech->has_tag_like(
p => qr(Reported by),
'OK: reporter information displayed'
);
}
$mech->get_ok('/history/=/4'); # print_and_exit();
{
for ('reported', 'new Molecular result summary') {
$mech->has_tag_like(
td => qr($_),
'OK: expected history present'
);
}
}
do_logout();
}
