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""" File contains endpoints for rqlt2"""
import shutil
from pathlib import Path
from flask import current_app
from flask import jsonify
from flask import Blueprint
from flask import request
from gn3.computations.rqtl2 import compose_rqtl2_cmd
from gn3.computations.rqtl2 import prepare_files
from gn3.computations.rqtl2 import validate_required_keys
from gn3.computations.rqtl2 import write_input_file
from gn3.computations.rqtl2 import process_qtl2_results
from gn3.computations.streaming import run_process
rqtl2 = Blueprint("rqtl2", __name__)
@rqtl2.route("/compute", methods=["POST"])
def compute():
"""Endpoint for computing QTL analysis using R/QTL2"""
data = request.json
required_keys = ["crosstype", "geno_data","pheno_data", "geno_codes"]
valid, error = validate_required_keys(required_keys,data)
if not valid:
return jsonify({"Error" : error}), 400
# Provide atleast one of this data entries.
if "pheno_map_data" not in data and "geno_map_data" not in data:
return jsonify({ "Error":"You need to Provide\
Either the Pheno map or Geno Map data"}), 400
run_id = request.args.get("id", "output")
# prepare necessary files and dir for computation
(workspace_dir, input_file,
output_file, log_file) = prepare_files(current_app.config.get("TMPDIR"))
# write the input file with data required for creating the cross
write_input_file(input_file, workspace_dir, data)
# TODO fix this
rqtl_path =Path(__file__).absolute().parent.parent.parent.joinpath("scripts/rqtl2_wrapper.R")
if not rqtl_path.is_file():
return jsonify({"error" : f"The script {rqtl_path} does not exists"}), 400
rqtl2_cmd = compose_rqtl2_cmd(rqtl_path, input_file,
output_file, workspace_dir,
data, current_app.config)
process_output = run_process(rqtl2_cmd.split(),log_file, run_id)
if process_output["code"] != 0:
return jsonify(process_output), 400
results = process_qtl2_results(output_file)
shutil.rmtree(workspace_dir, ignore_errors=True, onerror=None)
return jsonify(results)
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