add strain optional arg to Subject (#1241)

* remove validate_core_schema. You can check the core schema with e.g. * Update Subject unit test * Fix Subject unit test, add check for date_of_birth Co-authored-by: Ryan Ly <[email protected]>
NeurodataWithoutBorders · May 18, 2021 · 36a46b3 · 36a46b3
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commit 36a46b3
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Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/src/pynwb/file.py b/src/pynwb/file.py
@@ -44,7 +44,8 @@ class Subject(NWBContainer):
         'species',
         'subject_id',
         'weight',
-        'date_of_birth'
+        'date_of_birth',
+        'strain'
     )
 
     @docval({'name': 'age', 'type': str, 'doc': 'the age of the subject', 'default': None},
@@ -55,7 +56,8 @@ class Subject(NWBContainer):
             {'name': 'subject_id', 'type': str, 'doc': 'a unique identifier for the subject', 'default': None},
             {'name': 'weight', 'type': str, 'doc': 'the weight of the subject', 'default': None},
             {'name': 'date_of_birth', 'type': datetime, 'default': None,
-             'doc': 'datetime of date of birth. May be supplied instead of age.'})
+             'doc': 'datetime of date of birth. May be supplied instead of age.'},
+            {'name': 'strain', 'type': str, 'doc': 'the strain of the subject', 'default': None})
     def __init__(self, **kwargs):
         kwargs['name'] = 'subject'
         call_docval_func(super(Subject, self).__init__, kwargs)
@@ -66,6 +68,7 @@ def __init__(self, **kwargs):
         self.species = getargs('species', kwargs)
         self.subject_id = getargs('subject_id', kwargs)
         self.weight = getargs('weight', kwargs)
+        self.strain = getargs('strain', kwargs)
         date_of_birth = getargs('date_of_birth', kwargs)
         if date_of_birth and date_of_birth.tzinfo is None:
             self.date_of_birth = _add_missing_timezone(date_of_birth)

diff --git a/tests/integration/hdf5/test_nwbfile.py b/tests/integration/hdf5/test_nwbfile.py
@@ -203,14 +203,15 @@ class TestSubjectIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test Subject """
-        return Subject(age='12 mo',
+        return Subject(age='P90D',
                        description='An unfortunate rat',
                        genotype='WT',
                        sex='M',
                        species='Rattus norvegicus',
                        subject_id='RAT123',
                        weight='2 lbs',
-                       date_of_birth=datetime(1970, 1, 1, 12, tzinfo=tzutc()))
+                       date_of_birth=datetime(1970, 1, 1, 12, tzinfo=tzutc()),
+                       strain='my_strain')
 
     def addContainer(self, nwbfile):
         """ Add the test Subject to the given NWBFile """

diff --git a/tests/unit/test_file.py b/tests/unit/test_file.py
@@ -417,14 +417,15 @@ def test_multi_publications(self):
 
 class SubjectTest(TestCase):
     def setUp(self):
-        self.subject = Subject(age='12 mo',
+        self.subject = Subject(age='P90D',
                                description='An unfortunate rat',
                                genotype='WT',
                                sex='M',
                                species='Rattus norvegicus',
                                subject_id='RAT123',
                                weight='2 lbs',
-                               date_of_birth=datetime(2017, 5, 1, 12, tzinfo=tzlocal()))
+                               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',
@@ -438,13 +439,15 @@ def setUp(self):
                                subject=self.subject)
 
     def test_constructor(self):
-        self.assertEqual(self.subject.age, '12 mo')
+        self.assertEqual(self.subject.age, 'P90D')
         self.assertEqual(self.subject.description, 'An unfortunate rat')
         self.assertEqual(self.subject.genotype, 'WT')
         self.assertEqual(self.subject.sex, 'M')
         self.assertEqual(self.subject.species, 'Rattus norvegicus')
         self.assertEqual(self.subject.subject_id, 'RAT123')
         self.assertEqual(self.subject.weight, '2 lbs')
+        self.assertEqual(self.subject.date_of_birth, datetime(2017, 5, 1, 12, tzinfo=tzlocal()))
+        self.assertEqual(self.subject.strain, 'my_strain')
 
     def test_nwbfile_constructor(self):
         self.assertIs(self.nwbfile.subject, self.subject)