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""" File contains endpoints for rqlt2"""
import subprocess
import os
from flask import current_app
from flask import jsonify
from flask import Blueprint
from flask import request
rqtl2 = Blueprint("rqtl2", __name__)
@rqtl2.route("/compute", methods=["GET"])
def compute():
"""Endpoint for computing QTL analysis using R/QTL2"""
# get the run id to act as file identifier default to output
run_id = request.args.get("id", "output")
output_file = os.path.join(current_app.config.get("TMPDIR"),
f"{run_id}.txt")
# this should be computed locally not via files
rscript_cmd = (
"Rscript ./scripts/rqtl2_wrapper.R "
"-i /home/kabui/r_playground/meta_grav.json "
"-d /home/kabui/r_playground "
"-o /home/kabui/r_playground/rqtl_output.json "
"--nperm 100 --threshold 1 --cores 0"
)
process = subprocess.Popen(
rscript_cmd, shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT
)
for line in iter(process.stdout.readline, b""):
# these allow endpoint stream to read the file since
# no read and write file same tiem
with open(output_file, "a+", encoding="utf-8") as file_handler:
file_handler.write(line.decode("utf-8"))
process.stdout.close()
process.wait()
if process.returncode == 0:
return jsonify({"msg": "success",
"results": "file_here",
"run_id": run_id})
return jsonify({"msg": "fail",
"error": "Process failed",
"run_id": run_id})
@rqtl2.route("/stream/<identifier>", methods=["GET"])
def stream(identifier="output"):
""" 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"{identifier}.txt")
seek_position = int(request.args.get("peak", 0))
with open(output_file, encoding="utf-8") as file_handler:
# read to the last position default to 0
file_handler.seek(seek_position)
return jsonify({"data": file_handler.readlines(),
"run_id": identifier,
"pointer": file_handler.tell()})
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