def main():
# Parse arguments from the command line
parsed_args = parser_args()
# Check interpretation request ID matches expected pattern, and split into ID and version
ir_id, ir_version = get_request_details(parsed_args.interpretation_request)
# Get v6 of interpretation request JSON
ir_json_v6 = get_interpretation_request_json(
ir_id, ir_version, reports_v6=True, testing_on=parsed_args.testing)
# Check that there is only one exisitng clinical report
if num_existing_reports(ir_json_v6) != 1:
sys.exit(
"Expected 1 clinical report but found {num} for interpretation request {ir_id}-{ir_version}"
.format(num=num_existing_reports(ir_json_v6),
ir_id=ir_id,
ir_version=ir_version))
# Create exit questionnaire
eq = create_eq(eventDate=parsed_args.date,
reporter=parsed_args.reporter,
familyLevelQuestions=create_flq(
caseSolvedFamily="no",
segregationQuestion="no",
additionalComments="No tier 1 or 2 variants detected"))
# Push exit questionnaire to CIP-API
put_eq(exit_questionnaire=eq,
ir_id=ir_id,
ir_version=ir_version,
testing_on=parsed_args.testing)
def main():
# Parse arguments from the command line
parsed_args = parser_args()
# Check interpretation request ID matches expected pattern, and split into ID and version
ir_id, ir_version = get_request_details(parsed_args.interpretation_request)
# Get v6 of interpretation request JSON
ir_json_v6 = get_interpretation_request_json(ir_id, ir_version, reports_v6=True, testing_on=parsed_args.testing)
# Check that there is not already an exisitng clinical report
if num_existing_reports(ir_json_v6):
sys.exit("Existing clinical reports detected for interpretation request {ir_id}-{ir_version}".format(
ir_id=ir_id,
ir_version=ir_version
)
)
# Create clinical report object
cr = create_cr(
interpretationRequestId=ir_id,
interpretationRequestVersion=int(ir_version),
reportingDate=parsed_args.date,
user=parsed_args.reporter,
referenceDatabasesVersions=get_ref_db_versions(ir_json_v6),
softwareVersions=gel_software_versions(ir_json_v6),
genomicInterpretation="No tier 1 or 2 variants detected"
)
# Push clinical report to CIP-API
post_cr(clinical_report=cr, ir_json_v6=ir_json_v6, testing_on=parsed_args.testing)
def handle_interpretation_request(interpretation_request, force_update=False):
"""Handle an interpretation request for getting tiered variants.
Check if the interpretation request has interpretation_request_data and get
if from the CIPAPI if not. Make a simple_pedigree record and then pass the
interpretation_request to output_variant_tsv for export.
Args:
interpretation_request: JSON representation of an
interpretation_request (output of get_interpretation_request_json).
force_update: Boolean switch to enforce output file overwriting.
"""
# get_or_create interpretation_request_data
ir_id, ir_version = (
interpretation_request['interpretation_request_id'].split('-'))
try:
interpretation_request_data = (
interpretation_request['interpretation_request_data'])
except KeyError:
interpretation_request_data = (get_interpretation_request_json(
ir_id, ir_version))
interpretation_request['interpretation_request_data'] = (
interpretation_request_data)
# make simple pedigree
interpretation_request['simple_pedigree'] = (
get_pedigree_dict(interpretation_request))
output_variant_tsv(interpretation_request, force_update)
def test_get_irjson(jpconfig, authenticated_session):
"""Test that the interpretation request in config can be pulled from the CIPAPI"""
irid = jpconfig.get('pyCIPAPI', 'test_irid')
irversion = jpconfig.get('pyCIPAPI', 'test_irversion')
"""Interpretation request data can be downloaded from the CIPAPI with an authenticated session"""
data = irs.get_interpretation_request_json(irid,
irversion,
reports_v6=True,
session=authenticated_session)
assert 'interpretation_request_id' in data.keys()
def count_tiered_variants(case):
"""Count the number of variants in each tier for a case."""
case['T1'] = 0
case['T2'] = 0
case['T3'] = 0
ir_id, ir_version = case['interpretation_request_id'].split('-')
interpretation_request = get_interpretation_request_json(ir_id, ir_version)
case['interpretation-request_data'] = interpretation_request
for variant in (interpretation_request['interpretation_request_data']
['json_request']['TieredVariants']):
tier = get_variant_tier(variant)
case['T{}'.format(tier)] += 1
def get(cls: object, irid: int, irversion: int,
session: AuthenticatedCIPAPISession) -> IRJson:
"""Get an interpretation request json from the CPIAPI using jellypy.pyCIPAPI library
Args:
irid: Interpretation request id
irversion: Interpretation request version
session: An authenticated CIPAPI session (pyCIPAPI)
Returns:
An IRJson object
"""
json_response = irs.get_interpretation_request_json(irid,
irversion,
reports_v6=True,
session=session)
return IRJson(json_response)