#!/usr/bin/perl
# requires presence of config/.local/additional_tests.yml file, or skips tests
use Test::WWW::Mechanize::CGIApp;
use Test::Builder::Tester;
use Data::Dumper;
use strict;
use warnings;
use constant TESTS => 51;
use Test::More tests => TESTS;
# use Test::More 'no_plan';
=begin: tests:
=cut
BEGIN {
require 't/test-lib.pl';
}
my $yaml = get_yaml('additional_tests'); # warn Dumper $yaml; exit;
my $dbh;
eval {
$dbh = get_dbh() or die 'no database handle recieved from get_dbh';
};
my $dbix = get_dbix();
my $mech = get_mech();
SKIP: {
skip('these tests require config/.local/settings/additional_tests.yml file',TESTS) unless $yaml;
do_all_tests();
}
sub do_all_tests {
# need to see if 'require_spell_check' is required:
my $spell_check_required = is_spell_check_required(); # warn $spell_check_required;
# register data for auto_authorisation:
# get list of diagnoses from $yaml->{diagnosis}:
my $diagnosis = $yaml->{diagnosis};
my @diagnoses = keys %$diagnosis; # warn Dumper \@diagnoses; exit;
# select 1st entry:
my $new_diagnosis = $diagnoses[0]; # warn $new_diagnosis;
my $lab_test = $diagnosis->{$new_diagnosis}; # warn Dumper $lab_test;
# just add 1st diagnosis from $yaml:
$dbix->insert('diagnoses', {
name => $new_diagnosis, diagnostic_category_id => 1, active => 'yes',
});
# add new lab tests:
_add_lab_tests($lab_test);
do_login();
# 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:
$mech->get_ok('/screen/=/3'); # print_and_exit();
{
$mech->form_name('initialScreen'); # 1st one is patient notes
$mech->field(screen_id => 2); # PNH
$mech->field(option_id => 1);
$mech->submit(); # print_and_exit();
$mech->text_contains(
'Screened as PNH',
'OK: expected screen term found',
); # print_and_exit();
}
# sign out test:
$mech->get_ok('/worklist/display/1?display_format=Data+Entry'); # print_and_exit();
{
$mech->field(request_lab_test_id => 1);
$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 ( qw/PNH complete/ ) {
$mech->has_tag(td => $_);
} # print_and_exit();
}
# report - don't auto-request test (to demonstrate no [pending] fields):
$mech->get_ok('/report/=/3'); # print_and_exit();
{
my %report = ( # PB so doesn't need biopsy_site or gross_description
status => 'default',
clinical_details => 'some details here',
morphology => 'morphology here',
comment => 'comment here',
specimen_quality => 'adequate',
diagnosis_id => 2, # doesn't auto-request tests
);
$mech->form_name('reportForm');
$mech->submit_form(fields => \%report); # print_and_exit();
$mech->submit_form(form_name =>'reportForm') if $spell_check_required;
lacks_dfv_errors(); # print_and_exit();
$mech->has_tag_like(
p => qr(record updated successfully),
'OK: update success',
); # print_and_exit();
# check 'reported by':
$mech->has_tag_like(
p => qr(Reported by),
'OK: reporter information displayed'
);
# no pending tests:
{
test_out( 'not ok 1 - foo' );
test_fail( +1 );
$mech->has_tag_like( span => qr(\[pending\]), 'foo' );
test_test( 'OK: no pending lab-tests' ); # print_and_exit();
}
}
# change diagnosis to one auto-requesting tests:
$mech->get_ok('/report/=/3'); # print_and_exit();
{
$mech->form_name('reportForm');
$mech->field(diagnosis_id => 3); # auto-requests lab-test
$mech->field(option_id => 1);
$mech->submit(); # print_and_exit();
$mech->submit_form(form_name =>'reportForm') if $spell_check_required;
lacks_dfv_errors(); # print_and_exit();
$mech->text_contains(
$new_diagnosis,
'OK: changed diagnosis found',
); # print_and_exit();
$mech->has_tag_like(
p => qr(record updated successfully),
'OK: update success',
); # print_and_exit();
# check have requested test:
$mech->has_tag_like(
span => qr(\[pending\]),
'OK: new requested test'
); # print_and_exit();
}
# check history:
$mech->get_ok('/history/=/3'); # print_and_exit();
{
my $sql = 'select field_label from lab_tests where id = ?';
my @test_ids = keys %$lab_test; # warn Dumper \@test_ids;
# just test 1st one in case only 1 new test
$dbix->query($sql, $test_ids[0])->into(my $field_label); # warn $field_label;
$mech->has_tag_like(
td => qr(auto-requested $field_label triggered by diagnosis),
'OK: expected history entry'
); # print_and_exit();
}
#===============================================================================
# result summaries:
# get list of diagnoses from $yaml:
my $result_summary = $yaml->{results_summary}; # warn Dumper $result_summary;
my @result_summaries = keys %$result_summary; # warn Dumper \@result_summaries;
# select 1st entry:
my $rs_term = $result_summaries[0]; # warn $rs_term;
my $rs_lab_test = $result_summary->{$rs_term}; # warn Dumper $rs_lab_test;
# just add 1st result_summary term from $yaml:
$dbix->insert('result_summary_options', {
description => $rs_term, lab_section_id => 1, is_active => 'yes',
});
_add_lab_tests($rs_lab_test);
# 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 request:
$mech->get_ok('/screen/=/4'); # print_and_exit();
{
$mech->form_name('initialScreen'); # 1st one is patient notes
$mech->field(screen_id => 2); # PNH
$mech->field(option_id => 1);
$mech->submit(); # print_and_exit();
$mech->text_contains(
'Screened as PNH',
'OK: expected screen term found',
); # print_and_exit();
}
# sign out test:
$mech->get_ok('/worklist/display/1?display_format=Data+Entry'); # print_and_exit();
{
$mech->field(request_lab_test_id => 3);
$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 ( qw/PNH complete/ ) {
$mech->has_tag(td => $_);
} # print_and_exit();
}
# link tcr-gamma (250) with FISHpanel (34) to test linked lab-tests function:
$dbix->insert( 'linked_lab_test', { parent_test_id => 34, linked_test_id => 250 });
# have substituted non-ascii-numeric chars on field labels:
my @lab_tests_for_blpd_gcc = qw(t_14_18_multiplex FISH_panel Store_DNA tcr_gamma);
$mech->get_ok('/search/=/4'); # print_and_exit();
{
# no pending tests:
for ( @lab_tests_for_blpd_gcc ) {
test_out( 'not ok 1 - foo' );
test_fail( +1 );
$mech->has_tag_like( span => qr($_), 'foo' );
test_test( "OK: no pending $_ lab-test" ); # print_and_exit();
}
}
$mech->get_ok('/result/=/4'); # print_and_exit();
{
$mech->form_name('flow_results');
$mech->field(_results_summary => 'B-LPD - germinal centre phenotype (CD5-)');
$mech->submit(); # print_and_exit();
$mech->has_tag_like(
p => qr(results data update successful),
'OK: update success',
); # print_and_exit();
for ( @lab_tests_for_blpd_gcc ) {
$mech->has_tag_like(
span => qr{$_ \(new\)},
"OK: new $_ lab-test",
); # print_and_exit();
}
}
$mech->get_ok('/history/=/4'); # print_and_exit();
{
my $i = 1;
$mech->has_tag_like(
td => qr(new Flow result summary),
"OK: expected history entry [$i] found",
);
$i++;
for ( @lab_tests_for_blpd_gcc ) {
$mech->has_tag_like(
td => qq(auto-requested $_ triggered by results summary),
"OK: expected history entry [$i] found",
);
$i++;
}
}
do_logout();
}
sub _add_lab_tests {
my $data = shift;
my %h = ( # common lab_test fields:
lab_section_id => 1,
test_type => 'test',
has_results => 'no',
is_active => 'yes',
);
# lab_test_sample_type:
my $sample_type_ids = $dbix->select('lab_section_sample_type',
['sample_type_id'], { lab_section_id => 1 } )->flat; # warn Dumper $sample_type_ids;
while ( my($id, $test) = each %$data ) { # warn Dumper [$id, $test];
# skip if already exists:
next if $dbix->query('select 1 from lab_tests where id = ?', $id)->list;
$test =~ s/(\W)+/_/g; # eliminate non-ascii-numerical chars
@h{ qw(id field_label test_name) } = ( $id, $test, lc $test); # MUST USE SUPPLIED ID
$dbix->insert('lab_tests', \%h);
# lab_test_sample_type:
$dbix->insert('lab_test_sample_type',
{ lab_test_id => $id, sample_type_id => $_ }) for @$sample_type_ids;
}
}