A PHP package to transform your gnomics values into permissible values for commonly used CDEs within the CCDI API.
The values you have within your system may not match the permissible values for the CDEs. This package provides a way to transform your values into permissible values for the CDEs. As well as providing an AbstractTransformer class that can be extended to prodice custom transformations.
This package requires the following to work as expected:
- PHP 8.2.7
Optional:
- PHPUnit ^10.3
Install the package via composer:
composer require stjude/cde-transformers<?php
require_once __DIR__ . '/vendor/autoload.php';
use CCDI\Transformer\V0\SexTransformer;
$femalePermissibleValue = SexTransformer::transform('FEMALE')['permissible_value'];
?>Also see index.php for more examples.
A demo Customer Transform exists in src/Demo/AcmeHospital/AcmeSexTransformer.php. This can be used as a starting point for creating your own custom transformers.
This demo transformer has been created to transform the values of boy to the CDE value for Male and girl to the CDE value for Female.
Another example follows for transforming Swedish spelling of Normal:
class AcmeTissueTypeTransformer extends TissueTypeTransformer
{
public static function getMappings(): array
{
$mappings = TissueTypeTransformer::$MAPPINGS;
$mappings[] =
[
'value' => TissueType::NORMAL,
'regex' => '/^(vanligt)$/i'
];
return $mappings;
}
}Each CDE's permissible values, long name, concept code, CDE version, description CADsr URL, and public_id are harded coded into a Data class, e.g. src/CDE/V1/Data/Sex.php. This is to ensure that the permissible values are always up to date with the CDEs.
Once a CDE is released, a new version of the package can be released with the new permissible values, long names, etc.
Feel free to create a pull request to add new CDEs.
Run tests in tests/ using
vendor/bin/phpunit tests/
The MIT License (MIT). Please see License File for more information.