def upload():
if request.method == 'POST':
if 'vcf_file' not in request.files:
return jsonify({'msg': 'No vcf gzip part', 'table': []})
vcf_type = request.form['vcf_type']
vcf_file = request.files['vcf_file']
if vcf_file.filename == '':
return jsonify({'msg': 'No selected file', 'table': []})
if vcf_file and vcf_file.filename.rsplit('/')[-1][-6:] == 'vcf.gz':
# add timestamp
filename = '_'.join(
[str(int(time.time())),
secure_filename(vcf_file.filename)])
filepath = os.path.join(Config.VCF_FILE_PATH, filename)
vcf_file.save(filepath)
if os.stat(filepath).st_size > 1 * 1000:
task = async_fetch_vcf_samples.delay(filename,
current_user.username,
vcf_type)
redis_task.push_task(current_user.username, task.id)
return jsonify({'msg': 'async', 'task_id': task.id})
else:
result = fetch_vcf_samples(filename, vcf_type)
# write to mysql
for each in result:
row = Data(tc_id=each[0],
provider=current_user.username,
sample_name=each[1],
type=vcf_type)
row.save()
return jsonify({'msg': 'ok', 'table': result})
return jsonify({'msg': 'check upload file(only *.vcf.gz suffix)'})
def fetch_compare():
if request.method == 'POST':
info = request.form['info']
info = json.loads(info)
task = compare_info.delay(info)
redis_task.push_task(current_username(), task.id)
return jsonify({'msg': 'ok', 'task_id': task.id})
return jsonify({'msg': 'method not allowed'})
def fetch_query_result():
if request.method == 'POST':
info = request.form['info']
info = json.loads(info)
task = snp_info.delay(info)
if current_user.is_authenticated:
user_name = current_user.username
else:
user_name = 'anonymous'
redis_task.push_task(user_name, task.id)
return jsonify({'msg': 'ok', 'task_id': task.id})
return jsonify({'msg': 'method not allowed'})
def fetch_enrich_table():
if request.method == 'POST':
specie = request.form['specie']
gene_list = request.form.get('gene_list')
if gene_list:
gene_list = parseInput(gene_list)
if len(gene_list) > 20:
task = async_run_enrich.delay(specie, gene_list)
redis_task.push_task(current_user.username, task.id)
return jsonify({'msg': 'async', 'task_id': task.id})
result = run_enrich(specie, gene_list)
if len(result['body']) == 0:
return jsonify({
'msg': 'no enrich on your gene list.',
'result': {}
})
return jsonify({'msg': 'ok', 'result': result})
file = request.files['file']
filename = secure_filename(file.filename)
file.save(os.path.join(UPLOAD_FOLDER, 'enrich', filename))
task = async_run_enrich.delay(specie, filename)
return jsonify({'msg': 'async', 'task_id': task.id})
def fetch_bsa():
if request.method == 'POST':
info = request.form['info']
task = run_bsa.delay(info)
redis_task.push_task(current_username(), task.id)
return jsonify({'msg': 'ok', 'task_id': task.id})