add age__reference and adjust tests

CHANGELOG.md

@@ -6,7 +6,8 @@
 - Support explicit ordering of sphinx gallery tutorials in the docs. @oruebel (#1504), @bdichter (#1495)
 - Add developer guide on how to create a new tutorial. @oruebel (#1504)
 - Add images tutorial. @weiglszonja (#1470)
-- Add example code for s3fs in the streaming tutorial. @bdichter (#1499)
+- Add example code for fsspec in the streaming tutorial. @bdichter (#1499)
+- Add age__reference field. @bendichter ([#1540](https://github.com/NeurodataWithoutBorders/pynwb/pull/1540))
 
 ### Enhancements and minor changes
 - Update coverage workflow, report separate unit vs integration coverage. @rly (#1509)

src/pynwb/file.py

@@ -56,6 +56,13 @@ class Subject(NWBContainer):
     @docval({'name': 'age', 'type': str,
              'doc': ('The age of the subject. The ISO 8601 Duration format is recommended, e.g., "P90D" for '
                      '90 days old.'), 'default': None},
+            {
+                "name": "age__reference",
+                "type": str,
+                "doc": "Age is with reference to this event. Can be 'birth' or 'gestational'. If reference is "
+                       "omitted, 'birth' is implied.",
+                "default": "birth",
+            },
             {'name': 'description', 'type': str,
              'doc': 'A description of the subject, e.g., "mouse A10".', 'default': None},
             {'name': 'genotype', 'type': str,
@@ -78,6 +85,7 @@ class Subject(NWBContainer):
             {'name': 'strain', 'type': str, 'doc': 'The strain of the subject, e.g., "C57BL/6J"', 'default': None})
     def __init__(self, **kwargs):
         keys_to_set = ("age",
+                       "age__reference",
                        "description",
                        "genotype",
                        "sex",
@@ -87,8 +95,11 @@ def __init__(self, **kwargs):
                        "date_of_birth",
                        "strain")
         args_to_set = popargs_to_dict(keys_to_set, kwargs)
-        kwargs['name'] = 'subject'
-        super().__init__(**kwargs)
+        super().__init__(name="subject", **kwargs)
+
+        if args_to_set["age__reference"] is not None:
+            if args_to_set["age__reference"] not in ("birth", "gestational"):
+                raise ValueError("age__reference must be 'birth' or 'gestational'.")
 
         weight = args_to_set['weight']
         if isinstance(weight, float):

tests/unit/test_file.py

@@ -437,29 +437,35 @@ def test_multi_publications(self):
 
 class SubjectTest(TestCase):
     def setUp(self):
-        self.subject = Subject(age='P90D',
-                               description='An unfortunate rat',
-                               genotype='WT',
-                               sex='M',
-                               species='Rattus norvegicus',
-                               subject_id='RAT123',
-                               weight='2 kg',
-                               date_of_birth=datetime(2017, 5, 1, 12, tzinfo=tzlocal()),
-                               strain='my_strain')
+        self.subject = Subject(
+            age='P90D',
+            age__reference="birth",
+            description='An unfortunate rat',
+            genotype='WT',
+            sex='M',
+            species='Rattus norvegicus',
+            subject_id='RAT123',
+            weight='2 kg',
+            date_of_birth=datetime(2017, 5, 1, 12, tzinfo=tzlocal()),
+            strain='my_strain',
+        )
         self.start = datetime(2017, 5, 1, 12, tzinfo=tzlocal())
         self.path = 'nwbfile_test.h5'
-        self.nwbfile = NWBFile('a test session description for a test NWBFile',
-                               'FILE123',
-                               self.start,
-                               experimenter='A test experimenter',
-                               lab='a test lab',
-                               institution='a test institution',
-                               experiment_description='a test experiment description',
-                               session_id='test1',
-                               subject=self.subject)
+        self.nwbfile = NWBFile(
+            'a test session description for a test NWBFile',
+            'FILE123',
+            self.start,
+            experimenter='A test experimenter',
+            lab='a test lab',
+            institution='a test institution',
+            experiment_description='a test experiment description',
+            session_id='test1',
+            subject=self.subject,
+        )
 
     def test_constructor(self):
         self.assertEqual(self.subject.age, 'P90D')
+        self.assertEqual(self.subject.age__reference, "birth")
         self.assertEqual(self.subject.description, 'An unfortunate rat')
         self.assertEqual(self.subject.genotype, 'WT')
         self.assertEqual(self.subject.sex, 'M')
@@ -479,6 +485,10 @@ def test_weight_float(self):
         )
         self.assertEqual(subject.weight, '2.3 kg')
 
+    def test_age_reference_arg_check(self):
+        with self.assertRaisesWith(ValueError, "age__reference must be 'birth' or 'gestational'."):
+            Subject(subject_id='RAT123', age='P90D', age__reference='brth')
+
 
 class TestCacheSpec(TestCase):