view release on metacpan or  search on metacpan

t/19-cli-regression.t  view on Meta::CPAN

    unshift @cmd, $^X, $cli;
    push @cmd, '-O', '--test';

    my $actual_file = $case->{entity_output}
      ? File::Spec->catfile( $tmpdir, $case->{entity_output} )
      : $tmp_file;

    my ( $status, $output ) = run_cli(@cmd);
    diag($output) if $status != 0 && defined $output && length $output;
    is( $status, 0, "CLI $case->{name} exits successfully" );
    ok(
        compare_case_output( $case->{compare}, $case->{expected}, $actual_file ),
        "CLI $case->{name} matches reference output",
    );
}

{
    my $omop_dir = tempdir( CLEANUP => 1 );
    my @cmd = (
        $^X, $cli,
        '-ifhir', 't/fhir2bff/in/patient-bundle.json',
        '-oomop',
        '--out-dir', $omop_dir,
        '--ohdsi-db',
        '--path-to-ohdsi-db', $test_ohdsi_db_dir,
        '-O',
        '--test',
    );
    my ( $status, $output ) = run_cli(@cmd);
    diag($output) if $status != 0 && defined $output && length $output;
    is( $status, 0, 'CLI fhir2omop exits successfully' );

    for my $table (qw(
      CONDITION_OCCURRENCE
      DRUG_EXPOSURE
      MEASUREMENT
      OBSERVATION
      PERSON
      PROCEDURE_OCCURRENCE
    )) {
        ok(
            csv_files_match(
                "t/fhir2omop/out/$table.csv",
                File::Spec->catfile( $omop_dir, "$table.csv" ),
            ),
            "CLI fhir2omop $table matches reference output",
        );
    }
}

{
    my $tmp_file  = temp_output_file( suffix => '.json', dir => $tmpdir );
    my $input_file = temp_output_file( suffix => '.json', dir => $tmpdir );

    my $payload = {
        patient      => { id => 'openehr-patient-2' },
        compositions => [
            load_json_file('t/openehr2bff/in/gecco_personendaten.json'),
            load_json_file('t/openehr2bff/in/ips_canonical.json'),
            load_json_file('t/openehr2bff/in/laboratory_report.json'),
            load_json_file('t/openehr2bff/in/compo_corona.json'),
        ],
    };
    write_json_file( $input_file, $payload );

    my @cmd = ( $^X, $cli, '-iopenehr', $input_file, '-opxf', $tmp_file, '-O', '--test' );
    my ( $exit, $output ) = run_cli(@cmd);

    is( $exit, 0, 'CLI openehr2pxf exits successfully' )
      or diag $output;
    ok(
        structured_files_match( 't/openehr2pxf/out/pxf.json', $tmp_file ),
        'CLI openehr2pxf matches reference output'
    );
}

{
    my $tmp_file = temp_output_file( suffix => '.json', dir => $tmpdir );
    my @cmd = (
        $^X, $cli,
        '-ibff', 't/bff2pxf/in/individuals.json',
        '-opxf', $tmp_file,
        '--default-vital-status', 'UNKNOWN_STATUS',
        '-O',
        '--test',
    );

    my ( $status, $output ) = run_cli(@cmd);
    diag($output) if $status != 0 && defined $output && length $output;
    is( $status, 0, 'CLI bff2pxf accepts --default-vital-status' );

    my $pxf = load_json_file($tmp_file);
    is(
        $pxf->[0]{subject}{vitalStatus}{status},
        'UNKNOWN_STATUS',
        'CLI bff2pxf applies the configured default vitalStatus when no source value is available',
    );
}

done_testing();