def update_model_from_json(model_obj,
json,
user=None,
verbose=False,
allow_unknown_keys=False,
immutable_keys=None):
seqr_update_fields = {}
internal_fields = model_obj._meta.internal_json_fields if hasattr(
model_obj._meta, 'internal_json_fields') else []
for json_key, value in json.items():
orm_key = _to_snake_case(json_key)
if orm_key in (immutable_keys or []):
if allow_unknown_keys:
continue
raise ValueError('Cannot edit field {}'.format(orm_key))
if allow_unknown_keys and not hasattr(model_obj, orm_key):
continue
if getattr(model_obj, orm_key) != value:
if orm_key in internal_fields and not (user and user.is_staff):
raise ValueError(
'User {0} is not authorized to edit the internal field {1}'
.format(user, orm_key))
if verbose:
model_obj_name = getattr(model_obj, 'guid', model_obj.__name__)
logger.info("Setting {0}.{1} to {2}".format(
model_obj_name, orm_key, value))
seqr_update_fields[orm_key] = value
if seqr_update_fields:
update_seqr_model(model_obj, **seqr_update_fields)
def update_model_from_json(model_obj,
json,
user=None,
allow_unknown_keys=False,
immutable_keys=None):
immutable_keys = (immutable_keys or []) + [
'created_by', 'created_date', 'last_modified_date', 'id'
]
internal_fields = model_obj._meta.internal_json_fields if hasattr(
model_obj._meta, 'internal_json_fields') else []
has_updates = False
for json_key, value in json.items():
orm_key = _to_snake_case(json_key)
if orm_key in immutable_keys:
if allow_unknown_keys:
continue
raise ValueError('Cannot edit field {}'.format(orm_key))
if allow_unknown_keys and not hasattr(model_obj, orm_key):
continue
if getattr(model_obj, orm_key) != value:
if orm_key in internal_fields and not (user and user.is_staff):
raise PermissionDenied(
'User {0} is not authorized to edit the internal field {1}'
.format(user, orm_key))
has_updates = True
setattr(model_obj, orm_key, value)
if has_updates:
model_obj.save()
return has_updates
def _create_xbrowse_model(seqr_model, **kwargs):
try:
seqr_model_class = seqr_model.__class__
seqr_model_class_name = seqr_model_class.__name__
xbrowse_kwargs = convert_seqr_kwargs_to_xbrowse_kwargs(
seqr_model, **kwargs)
xbrowse_model_class = SEQR_TO_XBROWSE_CLASS_MAPPING[
seqr_model_class_name]
xbrowse_model_class_name = xbrowse_model_class.__name__
logging.info("_create_xbrowse_model(%s, %s)" %
(xbrowse_model_class_name, xbrowse_kwargs))
xbrowse_model = xbrowse_model_class.objects.create(**xbrowse_kwargs)
seqr_model_foreign_key_name = "seqr_" + _to_snake_case(
seqr_model_class_name)
if hasattr(xbrowse_model, seqr_model_foreign_key_name):
setattr(xbrowse_model, seqr_model_foreign_key_name, seqr_model)
xbrowse_model.save()
return xbrowse_model
except Exception as e:
logging.error("ERROR: error when creating xbrowse model %s: %s" %
(seqr_model, e))
traceback.print_exc()
return None
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_model_from_json(model_obj, json, user=None, verbose=False, allow_unknown_keys=False, immutable_keys=None, conditional_edit_keys=None):
immutable_keys = (immutable_keys or []) + ['created_by', 'created_date', 'last_modified_date', 'id']
seqr_update_fields = {}
internal_fields = model_obj._meta.internal_json_fields if hasattr(model_obj._meta, 'internal_json_fields') else []
for json_key, value in json.items():
orm_key = _to_snake_case(json_key)
if orm_key in immutable_keys:
if allow_unknown_keys:
continue
raise ValueError('Cannot edit field {}'.format(orm_key))
if allow_unknown_keys and not hasattr(model_obj, orm_key):
continue
if getattr(model_obj, orm_key) != value:
if orm_key in internal_fields and not (user and user.is_staff):
raise ValueError('User {0} is not authorized to edit the internal field {1}'.format(user, orm_key))
if conditional_edit_keys and orm_key in conditional_edit_keys:
conditional_edit_keys[orm_key](model_obj)
if verbose:
model_obj_name = getattr(model_obj, 'guid', None) or model_obj.__name__
logger.info("Setting {0}.{1} to {2}".format(model_obj_name, orm_key, value))
seqr_update_fields[orm_key] = value
if seqr_update_fields:
update_seqr_model(model_obj, **seqr_update_fields)
def _create_xbrowse_model(seqr_model, **kwargs):
try:
seqr_model_class = seqr_model.__class__
seqr_model_class_name = seqr_model_class.__name__
xbrowse_kwargs = convert_seqr_kwargs_to_xbrowse_kwargs(seqr_model, **kwargs)
xbrowse_model_class = SEQR_TO_XBROWSE_CLASS_MAPPING[seqr_model_class_name]
xbrowse_model_class_name = xbrowse_model_class.__name__
logging.info("_create_xbrowse_model(%s, %s)" % (xbrowse_model_class_name, xbrowse_kwargs))
xbrowse_model = xbrowse_model_class.objects.create(**xbrowse_kwargs)
seqr_model_foreign_key_name = "seqr_"+_to_snake_case(seqr_model_class_name)
if hasattr(xbrowse_model, seqr_model_foreign_key_name):
setattr(xbrowse_model, seqr_model_foreign_key_name, seqr_model)
xbrowse_model.save()
return xbrowse_model
except Exception as e:
logging.error("ERROR: error when creating xbrowse model %s: %s" % (seqr_model, e))
traceback.print_exc()
return None
def update_model_from_json(model_obj,
json,
user,
allow_unknown_keys=False,
immutable_keys=None,
updated_fields=None,
verbose=True):
immutable_keys = (immutable_keys or []) + [
'created_by', 'created_date', 'last_modified_date', 'id'
]
internal_fields = model_obj._meta.internal_json_fields if hasattr(
model_obj._meta, 'internal_json_fields') else []
if not updated_fields:
updated_fields = set()
for json_key, value in json.items():
orm_key = _to_snake_case(json_key)
if orm_key in immutable_keys:
if allow_unknown_keys:
continue
raise ValueError('Cannot edit field {}'.format(orm_key))
if allow_unknown_keys and not hasattr(model_obj, orm_key):
continue
if getattr(model_obj, orm_key) != value:
if orm_key in internal_fields and not user_is_analyst(user):
raise PermissionDenied(
'User {0} is not authorized to edit the internal field {1}'
.format(user, orm_key))
updated_fields.add(orm_key)
setattr(model_obj, orm_key, value)
if updated_fields:
model_obj.save()
if verbose:
log_model_update(logger, model_obj, user, 'update', updated_fields)
return bool(updated_fields)
def update_model_from_json(model_obj,
json,
user=None,
verbose=False,
allow_unknown_keys=False,
immutable_keys=None,
conditional_edit_keys=None):
immutable_keys = (immutable_keys or []) + [
'created_by', 'created_date', 'last_modified_date', 'id'
]
internal_fields = model_obj._meta.internal_json_fields if hasattr(
model_obj._meta, 'internal_json_fields') else []
for json_key, value in json.items():
orm_key = _to_snake_case(json_key)
if orm_key in immutable_keys:
if allow_unknown_keys:
continue
raise ValueError('Cannot edit field {}'.format(orm_key))
if allow_unknown_keys and not hasattr(model_obj, orm_key):
continue
if getattr(model_obj, orm_key) != value:
if orm_key in internal_fields and not (user and user.is_staff):
raise ValueError(
'User {0} is not authorized to edit the internal field {1}'
.format(user, orm_key))
if conditional_edit_keys and orm_key in conditional_edit_keys:
conditional_edit_keys[orm_key](model_obj)
if verbose:
model_obj_name = getattr(model_obj, 'guid',
None) or model_obj.__name__
logger.info("Setting {0}.{1} to {2}".format(
model_obj_name, orm_key, value))
setattr(model_obj, orm_key, value)
model_obj.save()
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])
