def get_fastq_individuals(store: Store, case_id: str = None) -> Iterator[str]:
"""Fetch individual ids from cases that are ready for SPRING compression"""
case_obj = store.family(case_id)
if not case_obj:
LOG.error("Could not find case %s", case_id)
raise CaseNotFoundError("")
for link_obj in case_obj.links:
yield link_obj.sample.internal_id
def export_sample(self, days: int = 0) -> str:
"""Export sample info."""
export_sample_parameters = ["export-sample", "-d", str(days)]
self.process.run_command(parameters=export_sample_parameters,
dry_run=self.dry_run)
output = self.process.stdout
# If sample not in genotype db, stdout of genotype command will be empty.
if not output:
raise CaseNotFoundError("samples not found in genotype db")
return output
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 export_sample_analysis(self, days: int = 0) -> str:
"""Export analysis."""
trending_call = self.base_call[:]
trending_call.extend(["export-sample-analysis", "-d", str(days)])
try:
LOG.info("Running Genotype API to get data.")
LOG.debug(trending_call)
output = subprocess.check_output(trending_call)
except CalledProcessError as error:
LOG.critical("Could not run command: %s", " ".join(trending_call))
raise error
output = output.decode("utf-8")
# If sample not in genotype db, stdout of genotype command will be empty.
if not output:
raise CaseNotFoundError("samples not found in genotype db")
return output