rc/2.11.3

[djkapner]

Description

write_behavior_nwb was failing on NWB checks.

• property indicator needed to be moved from BehaviorMetadata to BehaviorOphysMetadata
• the BehaviorJsonExtractor needed to share the code with BehaviorLimsExtractor for getting the stimulus_name from a pkl file.

Validations

1) This code snippet reproduced the observed error from production (and one other related to stimulus_name) and passes now in this branch.

import json
from allensdk.brain_observatory.behavior.write_behavior_nwb.__main__ import write_behavior_nwb

prod_injson_path = "/allen/programs/braintv/production/visualbehavior/prod2/specimen_900263316/behavior_session_928263200/BEHAVIOR_WRITE_NWB_QUEUE_928263200_input.json"
with open(prod_injson_path, "r") as f:
    j = json.load(f)

write_behavior_nwb(j["session_data"], "tmp.nwb")

2) This code snippet passes the assert and shows that this branch reproduces a released BehaviorSession

import json

from allensdk.brain_observatory.behavior.write_behavior_nwb.__main__ import write_behavior_nwb
from allensdk.brain_observatory.behavior.behavior_project_cache import VisualBehaviorOphysProjectCache
from allensdk.brain_observatory.behavior.behavior_session import BehaviorSession
from allensdk.brain_observatory.session_api_utils import sessions_are_equal


data_storage_directory = "/home/danielk/data"
cache = VisualBehaviorOphysProjectCache.from_s3_cache(
        cache_dir=data_storage_directory)
prod_session = cache.get_behavior_session(870987812)

prod_injson_path = "/allen/programs/braintv/production/visualbehavior/prod2/specimen_850862430/behavior_session_870987812/BEHAVIOR_WRITE_NWB_QUEUE_870987812_input.json"
with open(prod_injson_path, "r") as f:
    j = json.load(f)
write_behavior_nwb(j["session_data"], "tmp.nwb")

test_session = BehaviorSession.from_nwb_path("tmp.nwb")
assert sessions_are_equal(prod_session, test_session)

3. This snippet passes the assert and shows that this branch reproduces a released BehaviorOphysExperiment

import json
  
from allensdk.brain_observatory.behavior.write_nwb.__main__ import write_behavior_ophys_nwb
from allensdk.brain_observatory.behavior.behavior_project_cache import VisualBehaviorOphysProjectCache
from allensdk.brain_observatory.behavior.behavior_ophys_experiment import BehaviorOphysExperiment
from allensdk.brain_observatory.session_api_utils import sessions_are_equal


data_storage_directory = "/home/danielk/data"
cache = VisualBehaviorOphysProjectCache.from_s3_cache(
        cache_dir=data_storage_directory)
prod_experiment = cache.get_behavior_ophys_experiment(951980471)

prod_injson_path = "/allen/programs/braintv/production/neuralcoding/prod0/specimen_840355567/ophys_session_951410079/ophys_experiment_951980471/BEHAVIOR_OPHYS_WRITE_NWB_QUEUE_NO_STATE_CHANGE_951980471_input.json"
with open(prod_injson_path, "r") as f:
    j = json.load(f)
write_behavior_ophys_nwb(j["session_data"], "tmp.nwb", skip_eye_tracking=False)

test_experiment = BehaviorOphysExperiment.from_nwb_path("tmp.nwb")
assert sessions_are_equal(prod_experiment, test_experiment)

4) Bamboo tests are passing.

[danielsf]

LGTM