def _get_phenotips_username_and_password(user, project, permissions_level):
"""Checks if user has permission to access the given project, and raises an exception if not.
Args:
user (User): the django user object
project(Model): Project model
permissions_level (string): 'edit' or 'view'
Raises:
PermissionDenied: if user doesn't have permission to access this project.
Returns:
2-tuple: PhenoTips username, password that can be used to access patients in this project.
"""
if permissions_level == CAN_EDIT:
uname, pwd = get_phenotips_uname_and_pwd_for_project(
project.phenotips_user_id, read_only=False)
elif permissions_level == CAN_VIEW:
uname, pwd = get_phenotips_uname_and_pwd_for_project(
project.phenotips_user_id, read_only=True)
else:
raise ValueError("Unexpected auth_permissions value: %s" %
permissions_level)
auth_tuple = (uname, pwd)
return auth_tuple
def _create_patient_if_missing(project, individual):
"""Create a new PhenoTips patient record with the given patient id.
Args:
project (Model): seqr Project - used to retrieve PhenoTips credentials
individual (Model): seqr Individual
Returns:
True if patient created
Raises:
PhenotipsException: if unable to create patient record
"""
if phenotips_patient_exists(individual):
return False
url = '/rest/patients'
headers = {"Content-Type": "application/json"}
data = json.dumps({'external_id': individual.guid})
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id)
response_items = make_phenotips_api_call('POST', url, auth_tuple=auth_tuple, http_headers=headers, data=data, expected_status_code=201, parse_json_resonse=False)
patient_id = response_items['Location'].split('/')[-1]
logger.info("Created PhenoTips record with patient id {patient_id} and external id {external_id}".format(patient_id=patient_id, external_id=individual.guid))
username_read_only, _ = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=True)
_add_user_to_patient(username_read_only, patient_id, allow_edit=False)
logger.info("Added PhenoTips user {username} to {patient_id}".format(username=username_read_only, patient_id=patient_id))
individual.phenotips_patient_id = patient_id
individual.phenotips_eid = individual.guid
individual.save()
return True
def handle(self, *args, **options):
from_project = Project.objects.get(guid=options['from_project'])
to_project = Project.objects.get(guid=options['to_project'])
family_ids = options['family_ids']
families = Family.objects.filter(project=from_project,
family_id__in=family_ids)
print('Found {} out of {} families. No match for: {}.'.format(
len(families), len(set(family_ids)),
set(family_ids) - set([f.family_id for f in families])))
for f in families:
print("==> Moving phenotips for {}".format(f))
for seqr_individual in f.individual_set.all():
if phenotips_patient_exists(seqr_individual):
# make sure phenotips_patient_id is up to date
data_json = _get_patient_data(
from_project,
seqr_individual,
)
seqr_individual.phenotips_patient_id = data_json["id"]
seqr_individual.save()
# update permissions
phenotips_readonly_username, _ = get_phenotips_uname_and_pwd_for_project(
to_project.phenotips_user_id, read_only=True)
_add_user_to_patient(phenotips_readonly_username,
seqr_individual.phenotips_patient_id,
allow_edit=False)
phenotips_readwrite_username, _ = get_phenotips_uname_and_pwd_for_project(
to_project.phenotips_user_id, read_only=False)
_add_user_to_patient(phenotips_readwrite_username,
seqr_individual.phenotips_patient_id,
allow_edit=True)
for variant_tag_type in VariantTagType.objects.filter(
project=from_project):
variant_tags = VariantTag.objects.filter(
saved_variant__family__in=families,
variant_tag_type=variant_tag_type)
if variant_tags:
print('Updating "{}" tags'.format(variant_tag_type.name))
to_tag_type, created = VariantTagType.objects.get_or_create(
project=to_project, name=variant_tag_type.name)
if created:
to_tag_type.category = variant_tag_type.category
to_tag_type.description = variant_tag_type.description
to_tag_type.color = variant_tag_type.color
to_tag_type.order = variant_tag_type.order
to_tag_type.save()
variant_tags.update(variant_tag_type=to_tag_type)
print("Updating families")
families.update(project=to_project)
print("Done.")
def _enable_phenotips_for_project(project):
"""Creates 2 users in PhenoTips for this project (one that will be view-only and one that'll
have edit permissions for patients in the project).
"""
project.is_phenotips_enabled = True
project.phenotips_user_id = _slugify(project.name)
# view-only user
username, password = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=True)
create_phenotips_user(username, password)
# user with edit permissions
username, password = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=False)
create_phenotips_user(username, password)
project.save()
def update_individual_hpo_terms(request, individual_guid):
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
features = json.loads(request.body)
_create_patient_if_missing(project, individual)
patient_json = _get_patient_data(project, individual)
patient_json["features"] = features
patient_json_string = json.dumps(patient_json)
url = phenotips_patient_url(individual)
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=False)
make_phenotips_api_call('PUT', url, data=patient_json_string, auth_tuple=auth_tuple, expected_status_code=204)
phenotips_patient_id = patient_json['id']
phenotips_eid = patient_json.get('external_id')
individual.phenotips_data = json.dumps(patient_json)
individual.phenotips_patient_id = phenotips_patient_id
individual.phenotips_eid = phenotips_eid
individual.save()
return create_json_response({
individual.guid: {
'phenotipsData': patient_json,
'phenotipsPatientId': phenotips_patient_id,
'phenotipsEid': phenotips_eid
}
})
def _get_patient_data(project, individual):
"""Retrieves patient data from PhenoTips and returns a json obj.
Args:
project (Model): seqr Project - used to retrieve PhenoTips credentials
individual (Model): seqr Individual
Returns:
dict: json dictionary containing all PhenoTips information for this patient
Raises:
PhenotipsException: if unable to retrieve data from PhenoTips
"""
url = phenotips_patient_url(individual)
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id)
return make_phenotips_api_call('GET', url, auth_tuple=auth_tuple, verbose=False)
