Run this script by specifying the CSV file as an argument:
python add_subjects_from_csv.py subjects.csv
NOTE: this script assumes you have already added the required strains.
CSV FORMAT (example):
subject_id,sex,date_of_birth,strain_name,species
testcsv001,U,2020-02-01,C57BL/6J,Mus musculus
testcsv002,U,2020-02-01,C57BL/6J,Mus musculus
"""
import sys
import csv
import uobrainflex.utils.djconnect
from uobrainflex.pipeline import subject as subjectSchema
if len(sys.argv) < 2:
raise ValueError('You need to specify a CSV file with subject information.')
filename = sys.argv[1]
subjectTable = subjectSchema.Subject()
with open(filename) as csvfile:
reader = csv.DictReader(csvfile)
for oneSubject in reader:
subjectTable.insert1(oneSubject, skip_duplicates=True)
print(oneSubject)
"""
Provides an interface to add or delete items from a DataJoint database.
"""
from uobrainflex.utils import djtools
from uobrainflex.pipeline import subject as subjectSchema
from uobrainflex.pipeline import acquisition as acquisitionSchema
from uobrainflex.pipeline import experimenter as experimenterSchema
specialFormat = {'date_of_birth': 'YYYY-MM-DD', 'sex': 'M/F/U'}
subject = subjectSchema.Subject()
strain = subjectSchema.Strain()
species = subjectSchema.Species()
behaviorSession = acquisitionSchema.BehaviorSession()
lab = experimenterSchema.Lab()
experimenter = experimenterSchema.Experimenter()
tablesDict = {
'subject': subject,
'strain': strain,
'species': species,
'behavior_session': behaviorSession,
'lab': lab,
'experimenter': experimenter
}
tableNames = list(tablesDict)
# -- Get primary keys --
primaryKeys = []
for tableName, tableDB in tablesDict.items():
def submit_behavior_session(nwbFullpath):
"""
Add behavior session metadata to DataJoint database.
Args:
nwbFullpath (str): full path to NWB data file to register with the DJ.
Returns:
djBehaviorSession: DataJoint object pointing to the table of behavior sessions.
"""
# -- Load metadata from the NWB file --
ioObj = pynwb.NWBHDF5IO(nwbFullpath, 'r', load_namespaces=True)
nwbFileObj = ioObj.read()
#nwbFileObj = load.load_nwb_file(nwbFullpath)
sessionID = nwbFileObj.identifier
subject = nwbFileObj.subject.subject_id
experimenter = nwbFileObj.experimenter[0] # Use only first experimenter
startTime = nwbFileObj.session_start_time
sessionType = nwbFileObj.lab_meta_data['metadata'].session_type
trainingStage = nwbFileObj.lab_meta_data['metadata'].training_stage
behaviorVersion = nwbFileObj.lab_meta_data['metadata'].behavior_version
performance_dict = performance.get_summary(nwbFileObj)
licks_total = performance_dict['licks_total']
licks_left_ratio = performance_dict['licks_left_ratio']
choices_total = performance_dict['choices_total']
choices_left_stim_ratio = performance_dict['choices_left_stim_ratio']
hits_total = performance_dict['hits_total']
hits_left_ratio = performance_dict['hits_left_ratio']
hit_rate_left = performance_dict['hit_rate_left']
hit_rate_right = performance_dict['hit_rate_right']
ioObj.close()
filename = os.path.basename(nwbFullpath)
# -- Get access to the database tables --
djSubject = subjectSchema.Subject()
djExperimenter = experimenterSchema.Experimenter()
#djSessionType = acquisitionSchema.BehaviorSessionType()
#djTrainingStage = acquisitionSchema.BehaviorTrainingStage()
djBehaviorSession = acquisitionSchema.BehaviorSession()
if subject not in djSubject.fetch('subject_id'):
errMsg = 'You need to add new subjects manually before adding sessions.'
raise Exception(errMsg)
if experimenter not in djExperimenter.fetch('experimenter_id'):
errMsg = 'You need to add new experimenters manually before adding sessions.'
raise Exception(errMsg)
#djSessionType.insert1([sessionType], skip_duplicates=True)
#djTrainingStage.insert1([trainingStage], skip_duplicates=True)
# See pipeline.acquisition for order of attributes
newSession = (sessionID, subject, startTime, sessionType, trainingStage,
experimenter, filename, behaviorVersion, licks_total,
licks_left_ratio, choices_total, choices_left_stim_ratio,
hits_total, hits_left_ratio, hit_rate_left, hit_rate_right,
None)
# FIXME: currently it defaults to replace
djBehaviorSession.insert1(newSession, replace=True)
print("Submitted session '{}' to DataJoint.".format(sessionID))
return djBehaviorSession