class ShippingAPI:
"""Class to communicate with the tool shipping
Shipping is used as a unified tool for deploying in the Clinical Genomics environments
"""
def __init__(self, config: Dict[str, str]):
self.config = config
self.host_config = config["host_config"]
self.binary_path = config["binary_path"]
self.process = Process(binary=str(self.binary_path),
config=self.host_config,
config_parameter="--host-config")
self.dry_run = False
def set_dry_run(self, dry_run: bool) -> None:
"""Update dry run"""
LOG.info("Set dry run to %s", dry_run)
self.dry_run = dry_run
def deploy(self, app_name: str, app_config: Path = None):
"""Command to deploy a tool according to the specifications in the config files"""
LOG.info("Deploying the %s software", app_name)
deploy_args = []
if app_config:
LOG.info("Use app config %s", app_config)
deploy_args.extend(["--app-config", str(app_config)])
else:
deploy_args.extend(["--tool-name", app_name])
deploy_args.append("deploy")
self.process.run_command(deploy_args, dry_run=self.dry_run)
for line in self.process.stderr_lines():
LOG.info(line)
class LoqusdbAPI:
"""
API for loqusdb
"""
def __init__(self, config: dict, analysis_type: str = "wgs"):
super(LoqusdbAPI, self).__init__()
self.analysis_type = analysis_type
self.loqusdb_config = config["loqusdb"]["config_path"]
self.loqusdb_binary = config["loqusdb"]["binary_path"]
if self.analysis_type == "wes":
self.loqusdb_config = config["loqusdb-wes"]["config_path"]
self.loqusdb_binary = config["loqusdb-wes"]["binary_path"]
self.process = Process(self.loqusdb_binary, self.loqusdb_config)
def load(self,
family_id: str,
ped_path: str,
vcf_path: str,
gbcf_path: str,
vcf_sv_path: str = None) -> dict:
"""Add observations from a VCF."""
load_call_parameters = [
"load",
"-c",
family_id,
"-f",
ped_path,
"--variant-file",
vcf_path,
"--check-profile",
gbcf_path,
"--hard-threshold",
"0.95",
"--soft-threshold",
"0.90",
]
if self.analysis_type == "wgs" and vcf_sv_path:
load_call_parameters.extend(["--sv-variants", vcf_sv_path])
nr_variants = 0
self.process.run_command(load_call_parameters)
for line in self.process.stderr_lines():
line_content = line.split("INFO")[-1].strip()
if "inserted" in line_content:
nr_variants = int(line_content.split(":")[-1].strip())
return dict(variants=nr_variants)
def get_case(self, case_id: str) -> dict:
"""Find a case in the database by case id."""
case_obj = None
cases_parameters = ["cases", "-c", case_id, "--to-json"]
self.process.run_command(cases_parameters)
output = self.process.stdout
# If case not in loqusdb, stdout of loqusdb command will be empty.
if not output:
raise CaseNotFoundError(f"Case {case_id} not found in loqusdb")
case_obj = json.loads(output)[0]
return case_obj
def get_duplicate(self, vcf_file: str) -> dict:
"""Find matching profiles in loqusdb"""
ind_obj = {}
duplicates_params = [
"profile", "--check-vcf", vcf_file, "--profile-threshold", "0.95"
]
try:
self.process.run_command(duplicates_params)
except CalledProcessError:
# If CalledProcessError is raised, log and raise error
LOG.critical("Could not run profile command")
raise
output = self.process.stdout
if not output:
LOG.info("No duplicates found")
return ind_obj
ind_obj = json.loads(output)
return ind_obj
def __repr__(self):
return f"LoqusdbAPI(binary={self.loqusdb_binary}," f"config={self.loqusdb_config})"