def upload_vcf():
"""Write the uploaded file to a temporary directory and return its path."""
f = request.files['file']
if not f:
return error_response('Missing file', 'Must post a file to /upload')
if not f.filename.endswith('.vcf'):
return error_response('Invalid extension', 'File must end with .vcf')
tmp_dir = app.config['TEMPORARY_DIR']
dest_path = get_secure_unique_filename(f.filename, tmp_dir)
f.save(dest_path)
return 'file://' + dest_path
def examine(run_id):
with tables(db.engine, 'vcfs', 'bams') as (con, runs, bams):
q = select(runs.c).where(runs.c.id == run_id)
run = q.execute().fetchone()
if not run:
return error_response('Invalid run', 'Invalid run: %s' % run_id)
else:
run = dict(run)
run['spec'] = cycledash.api.genotypes.spec(run_id)
run['contigs'] = cycledash.api.genotypes.contigs(run_id)
# Ideally we could use e.g. cycledash.bams.Bam.get(bam_id)
for bam_type in ['normal', 'tumor']:
bam_id = run[bam_type + '_bam_id']
bam = bams.select(bams.c.id == bam_id).execute().fetchone()
if bam:
run[bam_type + '_bam'] = dict(bam)
del run[bam_type + '_bam_id']
return render_template('examine.html',
vcf=run,
vcfs=cycledash.api.runs.get_related_vcfs(run))
