def add_or_update_individuals_and_families(project, individual_records):
"""Add or update individual and family records in the given project.
Args:
project (object): Django ORM model for the project to add families to
individual_records (list): A list of JSON records representing individuals. See
pedigree_info_utils#convert_fam_file_rows_to_json(..)
"""
families = {}
for record in individual_records:
family, created = Family.objects.get_or_create(
project=project, family_id=record['familyId'])
if created:
if not family.display_name:
family.display_name = family.family_id
family.save()
logger.info("Created family: %s" % (family, ))
individual, created = Individual.objects.get_or_create(
family=family, individual_id=record['individualId'])
update_individual_from_json(individual,
record,
allow_unknown_keys=True)
# apply additional json fields which don't directly map to Individual model fields
individual.phenotips_eid = individual.guid # use this instead of individual_id to avoid chance of collisions
if created:
# create new PhenoTips patient record
patient_record = create_patient(project, individual.phenotips_eid)
individual.phenotips_patient_id = patient_record['id']
logger.info(
"Created PhenoTips record with patient id %s and external id %s"
% (str(individual.phenotips_patient_id),
str(individual.phenotips_eid)))
if record.get('hpoTerms'):
# update phenotips hpo ids
logger.info("Setting PhenoTips HPO Terms to: %s" %
(record.get('hpoTerms'), ))
set_patient_hpo_terms(project,
individual.phenotips_eid,
record.get('hpoTerms'),
is_external_id=True)
if not individual.display_name:
individual.display_name = individual.individual_id
individual.save()
_deprecated_update_original_individual_data(project, individual)
families[family.family_id] = family
# update pedigree images
for family in families.values():
update_pedigree_image(family)
def save_individuals_table(request, project_guid, token):
"""Handler for 'save' requests to apply Individual tables previously uploaded through receive_individuals_table(..)
Args:
request (object): Django request object
project_guid (string): project GUID
token (string): a token sent to the client by receive_individuals_table(..)
"""
project = _get_project_and_check_permissions(project_guid, request.user)
serialized_file_path = _compute_serialized_file_path(token)
with gzip.open(serialized_file_path) as f:
records = json.load(f)
families = {}
for record in records:
family, created = Family.objects.get_or_create(project=project, family_id=record['familyId'])
if created:
if not family.display_name:
family.display_name = family.family_id
family.save()
logger.info("Created family: %s" % str(family))
individual, created = Individual.objects.get_or_create(family=family, individual_id=record['individualId'])
update_individual_from_json(individual, record, allow_unknown_keys=True)
individual.phenotips_eid = individual.guid # use this instead of individual_id to avoid chance of collisions
if created:
patient_record = create_patient(project, individual.phenotips_eid)
individual.phenotips_patient_id = patient_record['id']
logger.info("Created phenotips record with patient id %s and external id %s" % (
str(individual.phenotips_patient_id), str(individual.phenotips_eid)))
if not individual.case_review_status:
individual.case_review_status = Individual.CASE_REVIEW_STATUS_IN_REVIEW
if not individual.display_name:
individual.display_name = individual.individual_id
individual.save()
_deprecated_update_original_individual_data(project, individual)
families[family.family_id] = family
# update pedigree images
for family in families.values():
update_pedigree_image(family)
# sync events
os.remove(serialized_file_path)
return create_json_response({})
def add_or_update_individuals_and_families(project,
individual_records,
user=None):
"""Add or update individual and family records in the given project.
Args:
project (object): Django ORM model for the project to add families to
individual_records (list): A list of JSON records representing individuals. See
the return value of pedigree_info_utils#convert_fam_file_rows_to_json(..)
Return:
2-tuple: updated_families, updated_individuals containing Django ORM models
"""
families = {}
updated_individuals = []
for i, record in enumerate(individual_records):
# family id will be in different places in the json depending on whether it comes from a flat uploaded file or from the nested individual object
family_id = record.get('familyId') or record.get('family',
{}).get('familyId')
if not family_id:
raise ValueError(
"record #%s doesn't contain a 'familyId' key: %s" %
(i, record))
if 'individualId' not in record and 'individualGuid' not in record:
raise ValueError(
"record #%s doesn't contain an 'individualId' key: %s" %
(i, record))
family, created = get_or_create_seqr_model(Family,
project=project,
family_id=family_id)
if created:
logger.info("Created family: %s", family)
if not family.display_name:
update_seqr_model(family, display_name=family.family_id)
# uploaded files do not have unique guid's so fall back to a combination of family and individualId
if record.get('individualGuid'):
individual_filters = {'guid': record['individualGuid']}
else:
individual_filters = {
'family': family,
'individual_id': record['individualId']
}
individual, created = get_or_create_seqr_model(Individual,
**individual_filters)
record['family'] = family
record.pop('familyId', None)
update_individual_from_json(individual,
record,
allow_unknown_keys=True,
user=user)
updated_individuals.append(individual)
# apply additional json fields which don't directly map to Individual model fields
individual.phenotips_eid = individual.guid # use guid instead of indiv_id to avoid collisions
if created:
# create new PhenoTips patient record
patient_record = create_patient(project, individual)
update_seqr_model(individual,
phenotips_patient_id=patient_record['id'],
case_review_status='I')
logger.info(
"Created PhenoTips record with patient id %s and external id %s"
% (str(individual.phenotips_patient_id),
str(individual.phenotips_eid)))
if record.get(JsonConstants.HPO_TERMS_PRESENT_COLUMN) or record.get(
JsonConstants.FINAL_DIAGNOSIS_OMIM_COLUMN):
# update phenotips hpo ids
logger.info("Setting PhenoTips HPO Terms to: %s" %
(record.get(JsonConstants.HPO_TERMS_PRESENT_COLUMN), ))
set_patient_hpo_terms(
project,
individual,
hpo_terms_present=record.get(
JsonConstants.HPO_TERMS_PRESENT_COLUMN, []),
hpo_terms_absent=record.get(
JsonConstants.HPO_TERMS_ABSENT_COLUMN, []),
final_diagnosis_mim_ids=record.get(
JsonConstants.FINAL_DIAGNOSIS_OMIM_COLUMN, []))
if not individual.display_name:
update_seqr_model(individual,
display_name=individual.individual_id)
families[family.family_id] = family
updated_families = list(families.values())
# update pedigree images
update_pedigree_images(updated_families)
return updated_families, updated_individuals
def add_or_update_individuals_and_families(project, individual_records):
"""Add or update individual and family records in the given project.
Args:
project (object): Django ORM model for the project to add families to
individual_records (list): A list of JSON records representing individuals. See
the return value of pedigree_info_utils#convert_fam_file_rows_to_json(..)
Return:
2-tuple: updated_families, updated_individuals containing Django ORM models
"""
families = {}
updated_individuals = []
for i, record in enumerate(individual_records):
if 'familyId' not in record:
raise ValueError(
"record #%s doesn't contain a 'familyId' key: %s" %
(i, record))
if 'individualId' not in record:
raise ValueError(
"record #%s doesn't contain an 'individualId' key: %s" %
(i, record))
family, created = Family.objects.get_or_create(
project=project, family_id=record['familyId'])
if created:
logger.info("Created family: %s", family)
if not family.display_name:
family.display_name = family.family_id
family.save()
individual, created = Individual.objects.get_or_create(
family=family, individual_id=record['individualId'])
update_individual_from_json(individual,
record,
allow_unknown_keys=True)
updated_individuals.append(individual)
# apply additional json fields which don't directly map to Individual model fields
individual.phenotips_eid = individual.guid # use guid instead of indiv_id to avoid collisions
if created:
# create new PhenoTips patient record
patient_record = create_patient(project, individual.phenotips_eid)
individual.phenotips_patient_id = patient_record['id']
individual.case_review_status = 'I'
logger.info(
"Created PhenoTips record with patient id %s and external id %s"
% (str(individual.phenotips_patient_id),
str(individual.phenotips_eid)))
if record.get('hpoTerms'):
# update phenotips hpo ids
logger.info("Setting PhenoTips HPO Terms to: %s" %
(record.get('hpoTerms'), ))
set_patient_hpo_terms(project,
individual.phenotips_eid,
record.get('hpoTerms'),
is_external_id=True)
if not individual.display_name:
individual.display_name = individual.individual_id
individual.save()
_deprecated_update_original_individual_data(project, individual)
families[family.family_id] = family
updated_families = list(families.values())
# update pedigree images
update_pedigree_images(updated_families)
return updated_families, updated_individuals