Merge pull request #87 from BIH-CEI/79-define-value-set-in-keyword-an…

…d-use-for-validation-of-datafieldinstance-and-datamodelinstance

validating values

src/phenopacket_mapper/data_standards/data_model.py

@@ -71,8 +71,12 @@ def validate(self) -> bool:
 
         :return: True if the instance is valid, False otherwise
         """
-        # TODO: Implement this method
-        raise NotImplementedError
+        if self.field.required and self.value is None:
+            return False
+        if self.value is not None and self.field.value_set:
+            if self.value in self.field.value_set:
+                return True
+        return False
 
 
 @dataclass(slots=True, frozen=True)

src/phenopacket_mapper/data_standards/value_set.py

@@ -85,6 +85,25 @@ def parse_value_set(
             compliance=compliance,
         )
 
+    def __contains__(self, item):
+        from phenopacket_mapper.data_standards import DataFieldValue
+        if isinstance(item, bool):
+            for element in self.elements:
+                if isinstance(element, bool) and element == item:
+                    return True
+        elif type(item) in [Coding, CodeableConcept, CodeSystem, str, int, float, Date, type]:
+            for element in self.elements:
+                if element == item:
+                    return True
+        elif isinstance(item, DataFieldValue):
+            for element in self.elements:
+                if element == item.value:
+                    return True
+        return False
+
+    def __iter__(self):
+        yield from self.elements
+
 
 TRUE_FALSE_VALUE_SET = ValueSet(name="TrueFalseValueSet",
                                 elements=[True, False],

tests/data_standards/test_value_set.py

@@ -0,0 +1,40 @@
+import pytest
+
+from phenopacket_mapper.data_standards import Coding, code_system, Date
+from phenopacket_mapper.data_standards.value_set import ValueSet
+
+
+@pytest.mark.parametrize("value, is_in, value_set", [
+    ('a', False, ValueSet(elements=[])),
+    ('a', False, ValueSet(elements=['A', 'b', 'c'])),
+    (Date, False, ValueSet(elements=['date', 'Date'])),
+    ('a', True, ValueSet(elements=['a', 'b', 'c'])),
+    ('test test 123', True, ValueSet(elements=['test test 123', 'b', 'c'])),
+    (3, True, ValueSet(elements=[3, 19, 7])),
+    (
+            Coding(system=code_system.SNOMED_CT, code='404684003'),
+            True,
+            ValueSet(elements=[Coding(system=code_system.SNOMED_CT, code='404684003'), 1, 'a'])
+    ),
+    (
+            code_system.HPO,
+            True,
+            ValueSet(elements=[
+                code_system.HPO, Coding(system=code_system.HPO, code="1"),
+                Coding(system=code_system.SNOMED_CT, code='404684003')
+            ])
+    ),
+    (False, False, ValueSet(elements=[0, 1])),
+    (True, False, ValueSet(elements=[0, 1])),
+    (True, True, ValueSet(elements=[True, False])),
+    (False, True, ValueSet(elements=[True, False])),
+    (0.117, True, ValueSet(elements=[0.117, 1.0])),
+    (str, True, ValueSet(elements=[str, int])),
+    (Date, True, ValueSet(elements=[Date, int])),
+    (Date(year=2024, month=9, day=18), True, ValueSet(elements=[Date(year=2024, month=9, day=18), 'date'])),
+])
+def test_in_valueset(value, is_in, value_set):
+    if is_in:
+        assert value in value_set
+    else:
+        assert value not in value_set