Change Age to dynamic per session.

Update unittest values.

allensdk/brain_observatory/behavior/data_objects/metadata/subject_metadata/age.py

@@ -1,18 +1,24 @@
+from datetime import datetime
 import re
 import warnings
 from typing import Optional
 
+import pytz
 from pynwb import NWBFile
 
 from allensdk.core import DataObject
 from allensdk.core import \
     JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
 from allensdk.internal.api import PostgresQueryMixin
+from allensdk.brain_observatory.behavior.data_objects.metadata\
+    .behavior_metadata.date_of_acquisition import \
+    DateOfAcquisition
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 
 
 class Age(DataObject, JsonReadableInterface, LimsReadableInterface,
           NwbReadableInterface):
-    """Age of animal (in days)"""
+    """Age (in days) of animal at the time the behavior session was taken."""
     def __init__(self, age: int):
         super().__init__(name="age_in_days", value=age)
 
@@ -25,17 +31,34 @@ def from_json(cls, dict_repr: dict) -> "Age":
     @classmethod
     def from_lims(cls, behavior_session_id: int,
                   lims_db: PostgresQueryMixin) -> "Age":
+        # TODO PSB-17: Need to likewise grab the daq from the stimulus
+        # file for now as the data for daq in LIMS needs to be
+        # updated.
+        date_of_acquisition = DateOfAcquisition.from_stimulus_file(
+            BehaviorStimulusFile.from_lims(
+                db=lims_db,
+                behavior_session_id=behavior_session_id).validate()
+        ).value
+
         query = f"""
-            SELECT a.name AS age
+            SELECT d.date_of_birth AS date_of_birth
             FROM behavior_sessions bs
             JOIN donors d ON d.id = bs.donor_id
-            JOIN ages a ON a.id = d.age_id
             WHERE bs.id = {behavior_session_id};
         """
-        age = lims_db.fetchone(query, strict=True)
-        age = cls._age_code_to_days(age=age)
+        date_of_birth = cls._check_timezone(
+            lims_db.fetchone(query, strict=True))
+
+        age = (date_of_acquisition - date_of_birth).days
         return cls(age=age)
 
+    @classmethod
+    def _check_timezone(cls, input_date: datetime) -> datetime:
+        if input_date.tzinfo is None:
+            # Add UTC tzinfo if not already set
+            input_date = pytz.utc.localize(input_date)
+        return input_date
+
     @classmethod
     def from_nwb(cls, nwbfile: NWBFile) -> "Age":
         age = cls._age_code_to_days(age=nwbfile.subject.age)

allensdk/test/brain_observatory/behavior/data_objects/metadata/test_behavior_ophys_metadata.py

@@ -129,41 +129,31 @@ def test_from_lims(self, meso):
             assert isinstance(bom.ophys_metadata, MultiplaneMetadata)
             assert bom.ophys_metadata.imaging_depth == 150
             assert bom.ophys_metadata.targeted_imaging_depth == 150
-            assert bom.behavior_metadata.session_type == "OPHYS_1_images_A"
-            assert (
-                bom.behavior_metadata.subject_metadata.reporter_line
-                == "Ai148(TIT2L-GC6f-ICL-tTA2)"
-            )
-            assert bom.behavior_metadata.subject_metadata.driver_line == [
-                "Sst-IRES-Cre"
-            ]
-            assert bom.behavior_metadata.subject_metadata.mouse_id == "457841"
-            assert (
-                bom.behavior_metadata.subject_metadata.full_genotype
-                == "Sst-IRES-Cre/wt;Ai148(TIT2L-GC6f-ICL-tTA2)/wt"
-            )
-            assert bom.behavior_metadata.subject_metadata.age_in_days == 233
-            assert bom.behavior_metadata.subject_metadata.sex == "F"
+
+            assert bom.behavior_metadata.session_type == 'OPHYS_1_images_A'
+            assert bom.behavior_metadata.subject_metadata.reporter_line == \
+                   'Ai148(TIT2L-GC6f-ICL-tTA2)'
+            assert bom.behavior_metadata.subject_metadata.driver_line == \
+                   ['Sst-IRES-Cre']
+            assert bom.behavior_metadata.subject_metadata.mouse_id == 457841
+            assert bom.behavior_metadata.subject_metadata.full_genotype == \
+                   'Sst-IRES-Cre/wt;Ai148(TIT2L-GC6f-ICL-tTA2)/wt'
+            assert bom.behavior_metadata.subject_metadata.age_in_days == 206
+            assert bom.behavior_metadata.subject_metadata.sex == 'F'
         else:
             assert isinstance(bom.ophys_metadata, OphysExperimentMetadata)
             assert bom.ophys_metadata.imaging_depth == 175
             assert bom.ophys_metadata.targeted_imaging_depth == 175
-            assert bom.behavior_metadata.session_type == "OPHYS_4_images_A"
-            assert (
-                bom.behavior_metadata.subject_metadata.reporter_line
-                == "Ai93(TITL-GCaMP6f)"
-            )
-            assert bom.behavior_metadata.subject_metadata.driver_line == [
-                "Camk2a-tTA",
-                "Slc17a7-IRES2-Cre",
-            ]
-            assert bom.behavior_metadata.subject_metadata.mouse_id == "491060"
-            assert (
-                bom.behavior_metadata.subject_metadata.full_genotype
-                == "Slc17a7-IRES2-Cre/wt;Camk2a-tTA/wt;Ai93(TITL-GCaMP6f)/wt"
-            )
-            assert bom.behavior_metadata.subject_metadata.age_in_days == 130
-            assert bom.behavior_metadata.subject_metadata.sex == "M"
+            assert bom.behavior_metadata.session_type == 'OPHYS_4_images_A'
+            assert bom.behavior_metadata.subject_metadata.reporter_line == \
+                   'Ai93(TITL-GCaMP6f)'
+            assert bom.behavior_metadata.subject_metadata.driver_line == \
+                   ['Camk2a-tTA', 'Slc17a7-IRES2-Cre']
+            assert bom.behavior_metadata.subject_metadata.mouse_id == 491060
+            assert bom.behavior_metadata.subject_metadata.full_genotype == \
+                   'Slc17a7-IRES2-Cre/wt;Camk2a-tTA/wt;Ai93(TITL-GCaMP6f)/wt'
+            assert bom.behavior_metadata.subject_metadata.age_in_days == 120
+            assert bom.behavior_metadata.subject_metadata.sex == 'M'
 
 
 class TestJson(TestBOM):