def post(self):
"""Create a new run.
This will import the VCF's genotypes into the database in a worker, as
well as annotate it with gene names.
"""
run = request.validated_body
try:
expect_one_of(request.validated_body, 'project_name', 'project_id')
except voluptuous.MultipleInvalid as e:
errors = [str(err) for err in e.errors]
abort(409, message='Validation error', errors=errors)
try:
projects.set_and_verify_project_id_on(run)
except voluptuous.Invalid as e:
abort(404, message='Project not found.', errors=[str(e)])
try:
_set_or_verify_bam_id_on(run, bam_type='normal')
_set_or_verify_bam_id_on(run, bam_type='tumor')
except voluptuous.Invalid as e:
abort(404, message='BAM not found.', errors=[str(e)])
with tables(db.engine, 'vcfs') as (con, runs):
run = runs.insert(
request.validated_body).returning(*runs.c).execute().fetchone()
workers.runner.start_workers_for_vcf_id(run['id'])
return dict(run), 201
def post(self):
"""Create a new BAM."""
try:
expect_one_of(request.validated_body, 'project_name', 'project_id')
except voluptuous.MultipleInvalid as e:
errors = [str(err) for err in e.errors]
abort(409, message='Validation error', errors=errors)
try:
projects.set_and_verify_project_id_on(request.validated_body)
except voluptuous.Invalid as e:
abort(404, message='Project not found.', error=str(e))
with tables(db.engine, 'bams') as (con, bams):
result = bams.insert(
request.validated_body).returning(*bams.c).execute()
bam = dict(result.fetchone())
return bam, 201
