def update_individual_handler(request, individual_guid):
"""Updates a single field in an Individual record.
Args:
request (object): Django HTTP Request object.
individual_guid (string): GUID of the Individual.
Request:
body should be a json dictionary like: { 'value': xxx }
Response:
json dictionary representing the updated individual like:
{
<individualGuid> : {
individualId: xxx,
sex: xxx,
affected: xxx,
...
}
}
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
update_individual_from_json(individual, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
individual.guid: _get_json_for_individual(individual, request.user)
})
def update_individual_field_handler(request, individual_guid, field_name):
"""Updates an Individual record.
Args:
individual_guid (string): GUID of the individual.
field_name (string): Name of Individual record field to update (eg. "affected").
"""
individual = Individual.objects.get(guid=individual_guid)
# check permission
project = individual.family.project
if not request.user.is_staff and not request.user.has_perm(
CAN_EDIT, project):
raise PermissionDenied("%s does not have EDIT permissions for %s" %
(request.user, project))
request_json = json.loads(request.body)
if "value" not in request_json:
raise ValueError("Request is missing 'value' key")
individual_json = {field_name: request_json['value']}
update_individual_from_json(individual, individual_json)
return create_json_response(
{individual.guid: _get_json_for_individual(individual, request.user)})
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 update_individual_field_handler(request, individual_guid, field_name):
"""Updates a single field in an Individual record.
Args:
request (object): Django HTTP Request object.
individual_guid (string): GUID of the Individual.
field_name (string): Name of the field to update (eg. "maternalId").
Request:
body should be a json dictionary like: { 'value': xxx }
Response:
json dictionary representing the updated individual like:
{
<individualGuid> : {
individualId: xxx,
maternalId: xxx,
affected: xxx,
...
}
}
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
if "value" not in request_json:
raise ValueError("Request is missing 'value' key: %s" %
(request.body, ))
individual_json = {field_name: request_json['value']}
update_individual_from_json(individual, individual_json)
return create_json_response(
{individual.guid: _get_json_for_individual(individual, request.user)})
def update_individual_field_handler(request, individual_guid, field_name):
"""Updates an Individual record.
Args:
individual_guid (string): GUID of the individual.
field_name (string): Name of Individual record field to update (eg. "affected").
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
if "value" not in request_json:
raise ValueError("Request is missing 'value' key: %s" %
(request.body, ))
individual_json = {field_name: request_json['value']}
update_individual_from_json(individual, individual_json)
return create_json_response(
{individual.guid: _get_json_for_individual(individual, request.user)})
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 = set()
parent_updates = []
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(JsonConstants.FAMILY_ID_COLUMN) or record.get('family', {}).get('familyId')
if not family_id:
raise ValueError("record #%s doesn't contain a 'familyId' key: %s" % (i, record))
if JsonConstants.INDIVIDUAL_ID_COLUMN not in record and 'individualGuid' not in record:
raise ValueError("record #%s doesn't contain an 'individualId' key: %s" % (i, record))
family = families.get(family_id)
if family:
created = False
else:
family, created = get_or_create_seqr_model(Family, project=project, family_id=family_id)
if created:
logger.info("Created family: %s", family)
# 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_id = record.get(JsonConstants.PREVIOUS_INDIVIDUAL_ID_COLUMN) or record[JsonConstants.INDIVIDUAL_ID_COLUMN]
individual_filters = {'family': family, 'individual_id': individual_id}
individual, created = get_or_create_seqr_model(Individual, **individual_filters)
if created:
record.update({
'caseReviewStatus': 'I',
})
record['family'] = family
record.pop('familyId', None)
if individual.family != family:
families[individual.family.family_id] = individual.family
if record.get(JsonConstants.PREVIOUS_INDIVIDUAL_ID_COLUMN):
updated_individuals.update(individual.maternal_children.all())
updated_individuals.update(individual.paternal_children.all())
record['displayName'] = ''
# Update the parent ids last, so if they are referencing updated individuals they will check for the correct ID
if record.get('maternalId') or record.get('paternalId'):
parent_updates.append({
'individual': individual,
'maternalId': record.pop('maternalId', None),
'paternalId': record.pop('paternalId', None),
})
update_individual_from_json(individual, record, allow_unknown_keys=True, user=user)
updated_individuals.add(individual)
families[family.family_id] = family
for update in parent_updates:
individual = update.pop('individual')
update_individual_from_json(individual, update, user=user)
updated_families = list(families.values())
# update pedigree images
update_pedigree_images(updated_families, project_guid=project.guid)
return updated_families, list(updated_individuals)
def add_or_update_individuals_and_families(project, individual_records, user):
"""
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
"""
updated_families = set()
updated_individuals = set()
parent_updates = []
family_ids = {_get_record_family_id(record) for record in individual_records}
families_by_id = {f.family_id: f for f in Family.objects.filter(project=project, family_id__in=family_ids)}
missing_family_ids = family_ids - set(families_by_id.keys())
for family_id in missing_family_ids:
family = create_model_from_json(Family, {'project': project, 'family_id': family_id}, user)
families_by_id[family_id] = family
updated_families.add(family)
individual_models = Individual.objects.filter(family__project=project).prefetch_related(
'family', 'mother', 'father')
has_individual_guid = any(record.get('individualGuid') for record in individual_records)
if has_individual_guid:
individual_lookup = {
i.guid: i for i in individual_models.filter(
guid__in=[record['individualGuid'] for record in individual_records])
}
else:
individual_lookup = defaultdict(dict)
for i in individual_models.filter(
individual_id__in=[_get_record_individual_id(record) for record in individual_records]):
individual_lookup[i.individual_id][i.family] = i
for record in individual_records:
family_id = _get_record_family_id(record)
family = families_by_id.get(family_id)
if has_individual_guid:
individual = individual_lookup[record.pop('individualGuid')]
else:
# uploaded files do not have unique guid's so fall back to a combination of family and individualId
individual_id = _get_record_individual_id(record)
individual = individual_lookup[individual_id].get(family)
if not individual:
individual = create_model_from_json(
Individual, {'family': family, 'individual_id': individual_id, 'case_review_status': 'I'}, user)
record['family'] = family
record.pop('familyId', None)
if individual.family != family:
family = individual.family
updated_families.add(family)
previous_id = record.pop(JsonConstants.PREVIOUS_INDIVIDUAL_ID_COLUMN, None)
if previous_id:
updated_individuals.update(individual.maternal_children.all())
updated_individuals.update(individual.paternal_children.all())
record['displayName'] = ''
# Update the parent ids last, so if they are referencing updated individuals they will check for the correct ID
if record.get('maternalId') or record.get('paternalId'):
parent_updates.append({
'individual': individual,
'maternalId': record.pop('maternalId', None),
'paternalId': record.pop('paternalId', None),
})
family_notes = record.pop(JsonConstants.FAMILY_NOTES_COLUMN, None)
if family_notes:
update_family_from_json(family, {'analysis_notes': family_notes}, user)
updated_families.add(family)
is_updated = update_individual_from_json(individual, record, user=user, allow_unknown_keys=True)
if is_updated:
updated_individuals.add(individual)
updated_families.add(family)
for update in parent_updates:
individual = update.pop('individual')
is_updated = update_individual_from_json(individual, update, user=user)
if is_updated:
updated_individuals.add(individual)
updated_families.add(individual.family)
# update pedigree images
update_pedigree_images(updated_families, user, project_guid=project.guid)
return list(updated_families), list(updated_individuals)
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
