def add_variants_task(req):
"""Perform the actual task of adding variants to the database after receiving an add request
Accepts:
req(flask.request): POST request received by server
"""
db = current_app.db
req_data = req.json
dataset_id = req_data.get("dataset_id")
samples = req_data.get("samples", [])
assembly = req_data.get("assemblyId")
filter_intervals = None
genes = req_data.get("genes")
if genes:
filter_intervals = compute_filter_intervals(req_data)
vcf_obj = extract_variants(
vcf_file=req_data.get("vcf_path"), samples=samples, filter=filter_intervals
)
nr_variants = count_variants(vcf_obj)
vcf_obj = extract_variants(
vcf_file=req_data.get("vcf_path"), samples=samples, filter=filter_intervals
)
added = variants_loader(
database=db,
vcf_obj=vcf_obj,
samples=set(samples),
assembly=assembly,
dataset_id=dataset_id,
nr_variants=nr_variants,
)
if added > 0:
# Update dataset object accordingly
update_dataset(database=db, dataset_id=dataset_id, samples=samples, add=True)
LOG.info(f"Number of inserted variants for samples:{samples}:{added}")
def variants(ds, sample):
"""Remove variants for one or more samples of a dataset"""
click.confirm(
f"Deleting variants for sample {sample}, dataset '{ds}'. Do you want to continue?",
abort=True,
)
# Make sure dataset exists and contains the provided sample(s)
dataset = current_app.db["dataset"].find_one({"_id": ds})
if dataset is None:
click.echo(f"Couldn't find any dataset with id '{ds}' in the database")
raise click.Abort()
for s in sample:
if s not in dataset.get("samples", []):
click.echo(f"Couldn't find any sample '{s}' in the sample list of dataset 'dataset'")
raise click.Abort()
updated, removed = delete_variants(current_app.db, ds, sample)
click.echo(f"Number of variants updated:{updated}, removed:{removed}")
if updated + removed > 0:
# remove sample(s) from dataset
update_dataset(database=current_app.db, dataset_id=ds, samples=list(sample), add=False)
def variants(ds, vcf, sample, panel):
"""Add variants from a VCF file to a dataset"""
# make sure dataset id corresponds to a dataset in the database
dataset = current_app.db["dataset"].find_one({"_id": ds})
if dataset is None:
click.echo(f"Couldn't find any dataset with id '{ds}' in the database")
raise click.Abort()
# Check if required sample(s) are contained in the VCF
vcf_samples = get_vcf_samples(vcf)
if not all(samplen in vcf_samples for samplen in sample):
click.echo(
f"One or more provided sample was not found in the VCF file. Valida samples are: { ','.join(vcf_samples)}"
)
raise click.Abort()
custom_samples = set(sample) # set of samples provided by users
filter_intervals = None
if len(panel) > 0:
# create BedTool panel with genomic intervals to filter VCF with
filter_intervals = merge_intervals(list(panel))
vcf_obj = extract_variants(vcf_file=vcf,
samples=custom_samples,
filter=filter_intervals)
if vcf_obj is None:
raise click.Abort()
nr_variants = count_variants(vcf_obj)
if nr_variants == 0:
click.echo("Provided VCF file doesn't contain any variant")
raise click.Abort()
vcf_obj = extract_variants(vcf_file=vcf,
samples=custom_samples,
filter=filter_intervals)
# ADD variants
added = add_variants(
database=current_app.db,
vcf_obj=vcf_obj,
samples=custom_samples,
assembly=dataset["assembly_id"],
dataset_id=ds,
nr_variants=nr_variants,
)
click.echo(f"{added} variants loaded into the database")
if added > 0:
# Update dataset object accordingly
update_dataset(database=current_app.db,
dataset_id=ds,
samples=custom_samples,
add=True)
def delete_variants_task(req):
"""Perform the actual task of removing variants from the database after receiving an delete request
Accepts:
req(flask.request): POST request received by server
"""
db = current_app.db
req_data = req.json
dataset_id = req_data.get("dataset_id")
samples = req_data.get("samples")
updated, removed = variant_deleter(db, dataset_id, samples)
if updated + removed > 0:
update_dataset(database=db, dataset_id=dataset_id, samples=samples, add=False)
LOG.info(f"Number of updated variants:{updated}. Number of deleted variants:{removed}")