# ========================== METADATA ==========================
# ==================== subject ====================
subject_info = {
c: nwb['general']['subject'][c].value.decode('UTF-8')
for c in ('subject_id', 'description', 'sex', 'species', 'weight',
'age', 'genotype')
}
# force subject_id to be lower-case for consistency
subject_info['subject_id'] = subject_info['subject_id'].lower()
# dob and sex
subject_info['sex'] = subject_info['sex'][0].upper()
dob_str = re.search('(?<=Date of birth:\s)(.*)',
subject_info['description'])
if utilities.parse_prefix(dob_str.group()) is not None:
subject_info['date_of_birth'] = utilities.parse_prefix(dob_str.group())
# source and strain
strain_str = re.search(
'(?<=Animal Strain:\s)(.*)', subject_info['description']
) # extract the information related to animal strain
if strain_str is not None: # if found, search found string to find matched strain in db
for s in subject.StrainAlias.fetch():
m = re.search(re.escape(s[0]), strain_str.group(), re.I)
if m is not None:
subject_info['strain'] = (subject.StrainAlias & {
'strain_alias': s[0]
}).fetch1('strain')
break
source_str = re.search(
print('=================================')
print(f'!!! ERROR LOADING FILE: {fname}')
print('=================================')
continue
# ========================== METADATA ==========================
# ==================== Subject ====================
subject_info = {c: nwb['general']['subject'][c].value.decode('UTF-8')
for c in ('subject_id', 'description', 'sex', 'species', 'age', 'genotype')}
# force subject_id to be lower-case for consistency
subject_info['subject_id'] = subject_info['subject_id'].lower()
# dob and sex
subject_info['sex'] = subject_info['sex'][0].upper()
dob_str = re.search('(?<=dateOfBirth:\s)(.*)(?=\n)', subject_info['description'])
if utilities.parse_prefix(dob_str.group()) is not None:
subject_info['date_of_birth'] = utilities.parse_prefix(dob_str.group())
# source and strain
strain_str = re.search('(?<=animalStrain:\s)(.*)', subject_info['description']) # extract the information related to animal strain
if strain_str is not None: # if found, search found string to find matched strain in db
for s in subject.StrainAlias.fetch():
m = re.search(re.escape(s[0]), strain_str.group(), re.I)
if m is not None:
subject_info['strain'] = (subject.StrainAlias & {'strain_alias': s[0]}).fetch1('strain')
break
source_str = re.search('(?<=animalSource:\s)(.*)', subject_info['description']) # extract the information related to animal strain
if source_str is not None: # if found, search found string to find matched strain in db
for s in reference.AnimalSourceAlias.fetch():
m = re.search(re.escape(s[0]), source_str.group(), re.I)
if m is not None: