def update_individual_hpo_terms(request, individual_guid):
"""Updates features fields for the given Individual
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
for feature_key in [
'features', 'absentFeatures', 'nonstandardFeatures',
'absentNonstandardFeatures'
]:
orm_key = _to_snake_case(feature_key)
value = [get_parsed_feature(feature) for feature in request_json[feature_key]] \
if request_json.get(feature_key) else None
setattr(individual, orm_key, value)
individual.save()
return create_json_response({
individual.guid:
_get_json_for_individual(individual,
request.user,
add_hpo_details=True)
})
def update_individual_hpo_terms(request, individual_guid):
"""Updates features fields for the given Individual
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
update_json = {
key:
[get_parsed_feature(feature)
for feature in request_json[key]] if request_json.get(key) else None
for key in [
'features', 'absentFeatures', 'nonstandardFeatures',
'absentNonstandardFeatures'
]
}
update_model_from_json(individual, update_json, user=request.user)
return create_json_response({
individual.guid:
_get_json_for_individual(individual,
request.user,
add_hpo_details=True)
})
def _update_individual_phenotips_fields(indiv, phenotips_json):
if phenotips_json.get('date_of_birth'):
indiv.birth_year = datetime.strptime(phenotips_json['date_of_birth'],
'%Y-%m-%d').year
if phenotips_json.get('life_status') == 'deceased':
indiv.death_year = datetime.strptime(phenotips_json['date_of_death'], '%Y-%m-%d').year \
if phenotips_json.get('date_of_death') else 0
if phenotips_json.get('global_age_of_onset'):
onset_label = phenotips_json['global_age_of_onset'][0]['label']
indiv.onset_age = seqr.models.Individual.ONSET_AGE_REVERSE_LOOKUP[
onset_label]
if phenotips_json.get('global_mode_of_inheritance'):
indiv.expected_inheritance = [
seqr.models.Individual.INHERITANCE_REVERSE_LOOKUP[i['label']]
for i in phenotips_json['global_mode_of_inheritance']
]
if phenotips_json['ethnicity']['maternal_ethnicity']:
indiv.maternal_ethnicity = phenotips_json['ethnicity'][
'maternal_ethnicity']
if phenotips_json['ethnicity']['paternal_ethnicity']:
indiv.paternal_ethnicity = phenotips_json['ethnicity'][
'paternal_ethnicity']
family_history = phenotips_json.get('family_history') or {}
if family_history.get('consanguinity') is not None:
indiv.consanguinity = family_history['consanguinity']
if family_history.get('affectedRelatives') is not None:
indiv.affected_relatives = family_history['affectedRelatives']
present_features = []
absent_features = []
nonstandard_features = []
absent_nonstandard_features = []
for feature in phenotips_json.get('features') or []:
feature_list = present_features if feature[
'observed'] == 'yes' else absent_features
feature_list.append(get_parsed_feature(feature))
for feature in phenotips_json.get('nonstandard_features') or []:
feature_list = nonstandard_features if feature[
'observed'] == 'yes' else absent_nonstandard_features
feature_list.append(
get_parsed_feature(feature,
feature_id=feature['label'],
additional_fields=['categories']))
if present_features:
indiv.features = present_features
if absent_features:
indiv.absent_features = absent_features
if nonstandard_features:
indiv.nonstandard_features = nonstandard_features
if absent_nonstandard_features:
indiv.absent_nonstandard_features = absent_nonstandard_features
if phenotips_json.get('disorders'):
mim_ids = map(lambda d: int(d['id'].lstrip('MIM:')),
phenotips_json['disorders'])
indiv.disorders = mim_ids
if phenotips_json.get('genes'):
indiv.candidate_genes = phenotips_json['genes']
if phenotips_json.get('rejectedGenes'):
indiv.rejected_genes = phenotips_json['rejectedGenes']
prenatal = phenotips_json['prenatal_perinatal_history']
for field in [
'assistedReproduction_fertilityMeds',
'assistedReproduction_iui',
'ivf',
'icsi',
'assistedReproduction_surrogacy',
'assistedReproduction_donoregg',
'assistedReproduction_donorsperm',
]:
if prenatal.get(field) is not None:
indiv_field = 'ar_{}'.format(
_to_snake_case(field.replace('assistedReproduction_', '')))
setattr(indiv, indiv_field, prenatal[field])