This is happening because you are doing async calls but handling it like it's sync. In angularjs, as in regular javascript, one solution to wait on async calls is to use promises.

In angularjs, promises are easy to create by the $q provider which will help you create new promises with the method defer(). Here's how you could implement it (remember to inject $q)

function byDepartment () {
    var deferred = $q.defer();
    var result = null;
    deparmentService.query({
        codDepartment: vm.codDepartment.codDepartment,
        reportBycodDepartment: 1
    }, function (data) {
        var success = JSON.stringify(data.success);
        if (success === false) {
            deferred.reject(data.message);
        } else {
            deferred.resolve(result.data);
        }
    });
    return deferred.promise;
}

When invoking the byDepartment() method you need to tell what should happend when the returned promise is succesful and when its not by passing one success function and one error function to the then() method on the promise

vm.updateChart = function () {
    vm.testValue = 0;
    if (!vm.codTestRoom) {
        console.log('consulta con departamento');
        byDepartment()
        .then(
            function (result) {
                vm.testValue = result;
            },
            function (message) {
                console.log(error);
            }
        );
    } else if (!vm.codEquipment) {
        console.log('Consulta con departamento y testRoom');
        vm.testValue = byDepartmentAndTestRoom();
    } else {
        console.log('Consulta con departamento, testRoom y Equipo');
        vm.testValue = byDepartmentAndTestRoomAndEquipment();
    }
    // console.log('Valor: ' + JSON.stringify(vm.testValue));
};