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"""Endpoints for running the rqtl cmd"""
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():
"""Given at least a geno_file and pheno_file, generate and
run the rqtl_wrapper script and return the results as JSON
"""
genofile = request.form['geno_file']
phenofile = request.form['pheno_file']
if not do_paths_exist([genofile, phenofile]):
raise FileNotFoundError
# Split kwargs by those with values and boolean ones that just convert to True/False
kwargs = ["model", "method", "nperm", "scale", "control_marker"]
boolean_kwargs = ["addcovar", "interval"]
all_kwargs = kwargs + boolean_kwargs
rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
rqtl_bool_kwargs = []
for kwarg in all_kwargs:
if kwarg in request.form:
if kwarg in kwargs:
rqtl_kwargs[kwarg] = request.form[kwarg]
if kwarg in boolean_kwargs:
rqtl_bool_kwargs.append(kwarg)
results = generate_rqtl_cmd(
rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
rqtl_wrapper_kwargs=rqtl_kwargs,
rqtl_wrapper_bool_kwargs=boolean_kwargs
)
return jsonify(results)
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