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Magma JS Introduction

The Magma Javascript API is there to allow accession of data and data dictionary in order to perform data cleansing, data harmonization, data filtering etc.

Syntax

Selectors and Execution context

The API offers a simple way to access to variables and variable value for a value set, based on Magma naming schema. A javascript is always defined within a context that defines implicitly the object to which the selection is applied.

See selectors description: $ and $var.

Chaining

Methods from this API return an object to which a method can be directly applied. This allow method calls chaining, for instance:

$('DO_YOU_SMOKE').any('DNK', 'PNA').not()

Using Selection Statements

To use JavaScript selection statements such as if-else and switch first convert Magma ScriptableValues to native JavaScript values using the .value() method. Here are some examples:

if-else

if($('BooleanType.blood.contraindicated').value()) {
   log('Blood collection has been contraindicated');
}
if($('IntegerType.tubes.collected').gt($('IntegerType.tubes.expected')).value()) {
   log('More tubes than expected.');
} else if ($('IntegerType.tubes.collected').lt($('IntegerType.tubes.expected')).value()) {
   log('Less tubes than expected.');
} else {
   log('Collected tubes matches expected tubes.');
}

switch

switch($('Admin.Participant.gender').value()) {
   case "MALE":
      log('Participant is male.');
   case "FEMALE":
      log('Participant is female.');
   default:
      log('Participant gender is unknown.');
}

Advanced Configuration

The javascript engine allows several levels of optimization, usually a compromise between compilation time and execution time.

The optimization level can be specified as a JVM system property, i.e. with the command line argument -Drhino.opt.level=<level> where level is a number between -1 (js code is interpreted) and 9 (js code is compiled and optimized as much as possible). See more about Rhino Optimization. In some rare cases the compilation can fail because the script is (very) large: in this situation the optimization level should be set to -1.