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):