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""" File contains endpoints for rqlt2"""
import subprocess
import uuid
import os
from flask import current_app
from flask import jsonify
from flask import Blueprint
rqtl2 = Blueprint("rqtl2", __name__)
@rqtl2.route("/compute", methods=["GET"])
def compute():
"""Endpoint for computing QTL analysis using R/QTL2"""
wkdir = current_app.config.get("TMPDIR")
output_file = os.path.join(wkdir, "output.txt")
rscript_cmd = (
f"Rscript ./scripts/rqtl2_wrapper.R "
f"-i /home/kabui/r_playground/meta_grav.json "
f"-d /home/kabui/r_playground "
f"-o /home/kabui/r_playground/rqtl_output.json "
f"--nperm 100 --threshold 1 --cores 0"
)
process = subprocess.Popen(
rscript_cmd, shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT
)
# TODO rethink where we write this file
with open(output_file, "a+") as file_handler:
for line in iter(process.stdout.readline, b""):
file_handler.write(line.decode("utf-8"))
process.stdout.close()
process.wait()
if process.returncode == 0:
return jsonify({"msg": "success", "results": "file_here"})
else:
return jsonify({"msg": "fail", "error": "Process failed"})
@rqtl2.route("/stream/<indetifier>", methods=["GET"])
def stream(indetifier):
""" This endpoints streams stdout from a file expects
the indetifier to be the file """
output_file = os.path.join(current_app.config.get("TMPDIR"),
f"{indetifier}.txt")
# raise error if file does not exist
with open(output_file) as file_handler:
# rethink how we do the read should this be stream / yield ????
return jsonify({"data": file_handler.readlines()})
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