def read_case(case_id: str, db: MongoAdapter = Depends(database)):
"""Return a specific case given petname ID"""
case = db.case({"case_id": case_id})
if not case:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND,
detail=f"Case {case_id} not found")
return JSONResponse(jsonable_encoder(Case(**case)),
status_code=status.HTTP_200_OK)
def build_case_object(
adapter: MongoAdapter,
case_id: str,
profile_path: Union[Path, str],
vcf_path: Union[Path, str],
vcf_sv_path: Union[Path, str] = None,
) -> Case:
"""Build case document and insert into the database, return resulting document"""
# Parse MAF profiles from profile files and save in the case object
profiles: dict = get_profiles(adapter=adapter, vcf_file=profile_path)
# Check if profiles have any duplicates in the database
check_profile_duplicates(adapter=adapter, profiles=profiles)
# CHeck that SNV file has GQ field
check_vcf_gq_field(vcf_path=vcf_path)
# CHeck that SNV file doesnt have SV variants
check_snv_variant_types(vcf_path=vcf_path)
individuals = {
sample: Individual(
ind_id=sample,
case_id=case_id,
ind_index=sample_index,
profile=profile,
)
for sample_index, (sample, profile) in enumerate(profiles.items())
}
individuals_list: List = list(individuals.values())
case_object = Case(
case_id=case_id,
profile_path=profile_path,
vcf_path=vcf_path,
vcf_sv_path=vcf_sv_path,
nr_sv_variants=0,
nr_variants=get_vcf_variant_count(vcf_path=vcf_path),
individuals=individuals_list,
inds=individuals,
id=case_id,
)
if vcf_sv_path:
case_object.nr_sv_variants = get_vcf_variant_count(vcf_path=vcf_sv_path)
case_object.sv_individuals = individuals_list
case_object.sv_inds = individuals
adapter.add_case(case_object.dict(by_alias=True, exclude={"id"}))
return Case(**adapter.case({"case_id": case_id}))
def delete_case(case_id: str, db: MongoAdapter = Depends(database)):
"""Delete a specific case given petname ID"""
existing_case = db.case({"case_id": case_id})
if not existing_case:
return JSONResponse(f"Case {case_id} does not exist",
status_code=status.HTTP_404_NOT_FOUND)
try:
delete(adapter=db,
case_obj=existing_case,
genome_build=settings.genome_build)
return JSONResponse(f"Case {case_id} had been deleted",
status_code=status.HTTP_200_OK)
except Exception as e:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
detail=
f"Error {e.__class__.__name__}: {e}; Case may be partially deleted",
)
def load_case(
case_id: str,
snv_file: str,
profile_file: str,
sv_file: Optional[str] = None,
db: MongoAdapter = Depends(database),
):
"""Upload a case to loqusdb"""
if db.case({"case_id": case_id}):
return JSONResponse(f"Case {case_id} already exists",
status_code=status.HTTP_409_CONFLICT)
if ((sv_file and not Path(sv_file).exists())
or not Path(snv_file).exists() or not Path(profile_file).exists()):
raise HTTPException(
detail="Input file path does not exist",
status_code=status.HTTP_406_NOT_ACCEPTABLE,
)
try:
case_object: Case = build_case_object(
case_id=case_id,
vcf_path=snv_file,
vcf_sv_path=sv_file,
profile_path=profile_file,
adapter=db,
)
insert_case_variants(adapter=db, case_obj=case_object)
return JSONResponse(jsonable_encoder(case_object),
status_code=status.HTTP_200_OK)
except LoqusdbAPIError as e:
LOG.error(e)
raise HTTPException(
detail=f"Exception {e.__class__.__name__}: {e.message}",
status_code=status.HTTP_400_BAD_REQUEST,
)
except Exception as e:
LOG.error(e)
raise HTTPException(
detail=f"Exception {e.__class__.__name__} {e}",
status_code=status.HTTP_400_BAD_REQUEST,
)