def _deprecated_update_original_family_fields(project, family, fields):
# also update base family
base_family = BaseFamily.objects.filter(
project__project_id=project.deprecated_project_id,
family_id=family.family_id)
base_family = base_family[0]
update_family_from_json(base_family, fields)
def update_family_field_handler(request, family_guid, field_name):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = 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")
value = request_json['value']
family_json = {field_name: value}
update_family_from_json(family, family_json)
_deprecated_update_original_family_record(project, family, field_name, value)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def update_family_field_handler(request, family_guid, field_name):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = 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, ))
value = request_json['value']
family_json = {field_name: value}
update_family_from_json(family, family_json)
_deprecated_update_original_family_field(project, family, field_name,
value)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def edit_families_handler(request, project_guid):
"""Edit or one or more Family records.
Args:
project_guid (string): GUID of project that contains these individuals.
"""
project = get_project_and_check_pm_permissions(project_guid, request.user)
request_json = json.loads(request.body)
if request_json.get('uploadedFileId'):
modified_families = load_uploaded_file(
request_json.get('uploadedFileId'))
else:
modified_families = request_json.get('families')
if modified_families is None:
return create_json_response({},
status=400,
reason="'families' not specified")
updated_families = []
for fields in modified_families:
if fields.get('familyGuid'):
family = Family.objects.get(project=project,
guid=fields['familyGuid'])
elif fields.get(PREVIOUS_FAMILY_ID_FIELD):
family = Family.objects.get(
project=project, family_id=fields[PREVIOUS_FAMILY_ID_FIELD])
else:
family, _ = get_or_create_model_from_json(
Family, {
'project': project,
'family_id': fields[FAMILY_ID_FIELD]
},
update_json=None,
user=request.user)
update_family_from_json(family,
fields,
user=request.user,
allow_unknown_keys=True)
updated_families.append(family)
updated_families_by_guid = {
'familiesByGuid': {
family.guid: _get_json_for_family(family,
request.user,
add_individual_guids_field=True)
for family in updated_families
}
}
return create_json_response(updated_families_by_guid)
def edit_families_handler(request, project_guid):
"""Edit or one or more Family records.
Args:
project_guid (string): GUID of project that contains these individuals.
"""
project = get_project_and_check_permissions(project_guid, request.user,
CAN_EDIT)
request_json = json.loads(request.body)
if 'form' not in request_json:
return create_json_response(
{}, status=400, reason="Invalid request: 'form' key not specified")
form_data = request_json['form']
modified_families_by_guid = form_data.get('modifiedFamilies')
if modified_families_by_guid is None:
return create_json_response(
{}, status=400, reason="'modifiedIndividuals' not specified")
# TODO more validation
#errors, warnings = validate_fam_file_records(modified_individuals_list)
#if errors:
# return create_json_response({'errors': errors, 'warnings': warnings})
updated_families = []
for familyGuid, fields in modified_families_by_guid.items():
family = Family.objects.get(project=project, guid=familyGuid)
update_family_from_json(family, fields)
updated_families.append(family)
for key, value in fields.items():
# TODO do this more efficiently
_deprecated_update_original_family_field(project, family, key,
value)
updated_families_by_guid = {
'familiesByGuid': {
family.guid: _get_json_for_family(family,
request.user,
add_individual_guids_field=True)
for family in updated_families
}
}
return create_json_response(updated_families_by_guid)
def update_family_fields_handler(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission - can be edited by anyone with access to the project
check_project_permissions(family.project, request.user)
request_json = json.loads(request.body)
update_family_from_json(family, request_json, user=request.user, allow_unknown_keys=True, immutable_keys=[
'family_id', 'display_name',
])
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def update_family_fields_handler(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = family.project
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
update_family_from_json(family, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def update_family_fields_handler(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
update_family_from_json(family, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def edit_families_handler(request, project_guid):
"""Edit or one or more Family records.
Args:
project_guid (string): GUID of project that contains these individuals.
"""
request_json = json.loads(request.body)
if request_json.get('uploadedFileId'):
modified_families = load_uploaded_file(request_json.get('uploadedFileId'))
else:
modified_families = request_json.get('families')
if modified_families is None:
return create_json_response(
{}, status=400, reason="'families' not specified")
project = get_project_and_check_permissions(project_guid, request.user, CAN_EDIT)
updated_families = []
for fields in modified_families:
if fields.get('familyGuid'):
family = Family.objects.get(project=project, guid=fields['familyGuid'])
elif fields.get(PREVIOUS_FAMILY_ID_FIELD):
family = Family.objects.get(project=project, family_id=fields[PREVIOUS_FAMILY_ID_FIELD])
else:
family, _ = get_or_create_seqr_model(Family, project=project, family_id=fields[FAMILY_ID_FIELD])
update_family_from_json(family, fields, user=request.user, allow_unknown_keys=True)
updated_families.append(family)
updated_families_by_guid = {
'familiesByGuid': {
family.guid: _get_json_for_family(family, request.user, add_individual_guids_field=True) for family in updated_families
}
}
return create_json_response(updated_families_by_guid)
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 = 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 = Family.objects.get_or_create(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 = Individual.objects.get_or_create(**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)
if record.get(JsonConstants.FAMILY_NOTES_COLUMN):
update_family_from_json(family, {'analysis_notes': record[JsonConstants.FAMILY_NOTES_COLUMN]})
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 _deprecated_update_original_family_fields(project, family, fields):
# also update base family
base_family = BaseFamily.objects.filter(
project__project_id=project.deprecated_project_id, family_id=family.family_id)
base_family = base_family[0]
update_family_from_json(base_family, fields)
