def get_or_create(self, model, **filters):
"""Get or create a record in the database.
Args:
session (Session): initialized database session
model (class): SQLAlchemy model for a table
filters (kwargs): filters to match records
Returns:
class, bool: model and weather it was created or not
"""
query = self.session.query(model).filter_by(**filters)
instance = query.first()
if instance:
return instance, False
else:
try:
params = {key: value for key, value in iteritems(filters)
if not isinstance(value, ClauseElement)}
instance = model(**params)
self.add(instance)
self.save()
return instance, True
except IntegrityError as exception:
self.session.rollback()
raise exception
def services():
"""Return registered services to interact with."""
services_dict = {}
for key, value in iteritems(current_app.config):
if key.endswith('_HOST'):
service_id = key.split('_')[0].lower()
services_dict[service_id] = value
return jsonify(services=services_dict)
def scout_config(self, cust_id, case_id, seq_type=None):
"""Build Scout config for a case/analysis."""
case_obj = self._get_case(cust_id, case_id, seq_type=seq_type)
scout_data = case_obj.scout_config_clinical()
for list_key, gene_list in iteritems(scout_data['gene_lists']):
if gene_list['date']:
gene_list['date'] = stringify_date(gene_list['date'])
return scout_data
def update_analysis(self, cust_id, case_id, **kwargs):
"""Update info for an existing analysis."""
analysis_obj = self._find_analysis(cust_id, case_id)
for field, value in iteritems(kwargs):
if field == 'finished_at':
analysis_obj.finished_at = dateify(value)
else:
setattr(analysis_obj, field, value)
self.db.save()
return analysis_obj.__json__()
def put(self, cust_id, case_id):
"""Update info for an existing analysis."""
analysis_obj = utils.latest_analysis(cust_id, case_id)
for field, value in iteritems(request.form):
if field == 'finished_at':
analysis_obj.finished_at = dateify(value)
elif field == 'was_successful':
value = False if value.lower() == 'false' else True
analysis_obj.was_successful = value
else:
setattr(analysis_obj, field, value)
db.session.commit()
return analysis_obj.to_json()
def post_coverage(cust_id, case_id):
"""Load coverage for all samples in a case."""
analysis_res = glue.get("analyze", "analyses", cust_id, case_id)
samples = []
for sample_id, bed_file in iteritems(analysis_res.json["chanjo_output"]):
sample_res = glue.get("lims", "samples", sample_id)
# use customer sample id
alt_id = sample_res.json["name"]
load_payload = {"bed_file": bed_file, "sample_id": alt_id, "group_id": case_id}
glue.post("chanjo", "samples", data=load_payload)
samples.append(sample_res.json)
return samples
def _external_ped(self, ped_individuals):
id_mapping = self._map_sample_ids(ped_individuals)
external_individuals = {}
for individual_id, individual in iteritems(ped_individuals):
external_id = id_mapping.get(individual_id)
individual.individual_id = external_id
individual.mother = id_mapping.get(individual.mother, '0')
individual.father = id_mapping.get(individual.father, '0')
# all individuals in the pedigree have been sequenced
individual.consultand = 'Yes'
external_individuals[external_id] = individual
return external_individuals
def post(self):
"""Load a case into Scout."""
variant_threshold = request.form.get('variant_threshold', 5000)
variant_type = request.form.get('variant_type', 'clinical')
vcf_config = (request.form.get('vcf_config') or
current_app.config['SCOUT_VCF_CONFIG'])
mongo_info = current_app.config['SCOUT_MONGODB_SETTINGS']
mongo_auth = {}
for key, value in iteritems(mongo_info):
if key == 'db':
mongo_auth['mongo_db'] = value
else:
mongo_auth[key] = value
scout_config_path = request.form['scout_config']
scout_config = ConfigParser(scout_config_path)
load_mongo_db(scout_config, vcf_config, variant_type=variant_type,
variant_number_threshold=variant_threshold, **mongo_auth)
return jsonify(success=True)
def load_case(
self, scout_config_path, variant_type="clinical", vcf_config=None, variant_threshold=5000, mongo_auth=None
):
"""Load a case into Scout."""
vcf_config = vcf_config or self.config["scout"]["vcf_config"]
if mongo_auth is None:
# adapt to scout input
mongo_info = self.config["scout"]["auth"]
mongo_auth = {}
for key, value in iteritems(mongo_info):
if key == "db":
mongo_auth["mongo_db"] = value
else:
mongo_auth[key] = value
scout_config = ConfigParser(scout_config_path)
vcf = load_mongo_db(
scout_config,
vcf_config,
variant_type=variant_type,
variant_number_threshold=variant_threshold,
**mongo_auth
)
return vcf
def _map_sample_ids(self, ped_individuals):
"""Map between internal and external sample ids."""
id_mapping = {ind_id: (ind.extra_info.get('display_name') or ind_id)
for ind_id, ind in iteritems(ped_individuals)}
return id_mapping
def init_app(self, app):
"""Initialize Flask plugin."""
self.hosts = {key.split('_')[0].lower(): value
for key, value in iteritems(app.config)
if key.endswith('_HOST')}