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t/01-api-bff-pxf.t  view on Meta::CPAN

    {
        name     => 'pxf2jsonf',
        method   => 'pxf2jsonf',
        in_file  => 't/pxf2bff/in/pxf.json',
        out_file => 't/pxf2jsonf/out/pxf.fold.json',
        writer   => 'json',
    },
);

for my $case (@cases) {
    my $tmp_file = temp_output_file(
        suffix => $case->{writer} eq 'csv' ? '.csv' : '.json'
    );

    my $convert = build_convert(
        in_file  => $case->{in_file},
        out_file => $tmp_file,
        method   => $case->{method},
    );

    if ( $case->{writer} eq 'csv' ) {
        my $data = $convert->${ \$case->{method} };
        my $headers = get_headers($data);
        write_csv_rows( $tmp_file, $headers, $data );
    }
    else {
        my $suffix = $case->{out_file} =~ /\.ya?ml$/ ? '.yaml' : '.json';
        $tmp_file =~ s/\.[^.]+$/$suffix/;
        write_json_file( $tmp_file, $convert->${ \$case->{method} } );
    }

    my $match =
      $case->{writer} eq 'csv'
      ? Test::ConvertPheno::json_files_match( $case->{out_file}, $tmp_file )
      : structured_files_match( $case->{out_file}, $tmp_file );
    ok( $match, $case->{name} );
}

{
    my $bff = read_first_json_object('t/bff2pxf/in/individuals.json');
    my $pxf = read_first_json_object('t/bff2pxf/out/pxf.json');

    $pxf->{$_} = undef for qw(id metaData);

    my $convert = build_convert(
        in_textfile => 0,
        data        => $bff,
        method      => 'bff2pxf',
    );

    my $got = $convert->bff2pxf;
    $got->{$_} = undef for qw(id metaData);

    is_deeply( $got, $pxf, 'bff2pxf module conversion matches fixture' );
}

{
    my $gender = load_json_file('t/openehr2bff/in/gecco_personendaten.json');
    my $ips    = load_json_file('t/openehr2bff/in/ips_canonical.json');
    my $lab    = load_json_file('t/openehr2bff/in/laboratory_report.json');
    my $corona = load_json_file('t/openehr2bff/in/compo_corona.json');

    my $convert = build_convert(
        method      => 'openehr2pxf',
        data        => {
            patient      => { id => 'openehr-patient-2' },
            compositions => [ $gender, $ips, $lab, $corona ],
        },
        in_textfile => 0,
    );

    my $tmp_file = temp_output_file( suffix => '.json' );
    write_json_file( $tmp_file, $convert->openehr2pxf );
    ok(
        structured_files_match( 't/openehr2pxf/out/pxf.json', $tmp_file ),
        'openehr2pxf module conversion matches fixture'
    );
}

{
    my $patient_a = load_json_file('t/openehr2bff/in/gecco_personendaten.json');
    my $patient_b = load_json_file('t/openehr2bff/in/gecco_personendaten.json');

    $patient_a->{subject} = {
        _type        => 'PARTY_SELF',
        external_ref => {
            id        => { _type => 'GENERIC_ID', value => 'patient-a', scheme => 'PMI' },
            namespace => 'PMI',
            type      => 'PERSON',
        },
    };
    $patient_b->{subject} = {
        _type        => 'PARTY_SELF',
        external_ref => {
            id        => { _type => 'GENERIC_ID', value => 'patient-b', scheme => 'PMI' },
            namespace => 'PMI',
            type      => 'PERSON',
        },
    };

    my $convert = build_convert(
        method      => 'openehr2pxf',
        data        => [
            { compositions => [$patient_a] },
            { compositions => [$patient_b] },
        ],
        in_textfile => 0,
    );

    my $pxf = $convert->openehr2pxf;
    is( ref($pxf), 'ARRAY', 'openehr2pxf returns an array for multi-patient input' );
    is( scalar @{$pxf}, 2, 'openehr2pxf emits one phenopacket per patient bucket' );
}

{
    my $bff = {
        id   => 'subject-1',
        sex  => { id => 'NCIT:C20197', label => 'male' },
        info => {
            phenopacket => {
                dateOfBirth    => '1980-01-02',
                biosamples     => [ { id => 'bio-1' } ],
                interpretations => [ { id => 'int-1' } ],
                files          => [ { uri => 'file://example' } ],
                genes          => [ { id => 'HGNC:5' } ],
                variants       => [ { id => 'var-1' } ],
                pedigree       => { id => 'ped-1' },