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import os
from flask import Blueprint
from flask import current_app
from flask import jsonify
from flask import request
from gn3.computations.rqtl import generate_rqtl_cmd
from gn3.computations.gemma import do_paths_exist
rqtl = Blueprint("rqtl", __name__)
@rqtl.route("/compute", methods=["POST"])
def compute():
working_dir = os.path.join(current_app.config.get("TMPDIR"))
genofile = request.form['geno_file']
phenofile = request.form['pheno_file']
if not do_paths_exist([genofile, phenofile]):
raise FileNotFoundError
kwarg_list = ["addcovar", "model", "method", "interval", "nperm", "scale", "control_marker"]
rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
for kwarg in kwarg_list:
if kwarg in request.form:
rqtl_kwargs[kwarg] = request.form[kwarg]
results = generate_rqtl_cmd(
rqtl_wrapper_cmd = current_app.config.get("RQTL_WRAPPER_CMD"),
output_dir = current_app.config.get('TMPDIR'),
rqtl_wrapper_kwargs = rqtl_kwargs
)
return jsonify(results)
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