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"""Endpoints for running the rqtl cmd"""
import os
import uuid
import subprocess
from pathlib import Path
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, process_rqtl_mapping, \
process_rqtl_pairscan, process_perm_output
from gn3.fs_helpers import assert_path_exists, get_tmpdir
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']
assert_path_exists(genofile)
assert_path_exists(phenofile)
run_id = request.args.get("id")
with open(os.path.join(current_app.config.get("TMPDIR"),
f"{run_id}.txt"), "w+", encoding="utf-8"):
# TODO thos should be refactored
pass
# Split kwargs by those with values and boolean ones
# that just convert to True/False
kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control"]
boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"]
all_kwargs = kwargs + boolean_kwargs
rqtl_kwargs = {"geno": genofile, "pheno": phenofile, "outdir": current_app.config.get("TMPDIR")}
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)
outdir = os.path.join(get_tmpdir(), "gn3")
if not os.path.isdir(outdir):
os.mkdir(outdir)
rqtl_cmd = generate_rqtl_cmd(
rqtl_wrapper_cmd=str(
Path(__file__).absolute().parent.parent.parent.joinpath(
'scripts/rqtl_wrapper.R')),
rqtl_wrapper_kwargs=rqtl_kwargs,
rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs
)
rqtl_output = {}
# get the stdout file
run_id = request.args.get("id", str(uuid.uuid4()))
if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"),
"gn3", rqtl_cmd.get('output_file'))):
pass
stream_ouput_file = os.path.join(current_app.config.get("TMPDIR"),
f"{run_id}.txt")
run_process(rqtl_cmd.get("rqtl_cmd"), stream_ouput_file, run_id)
if "pairscan" in rqtl_bool_kwargs:
rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'), genofile)
else:
rqtl_output['results'] = process_rqtl_mapping(rqtl_cmd.get('output_file'))
if int(rqtl_kwargs['nperm']) > 0:
# pylint: disable=C0301
rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = process_perm_output(rqtl_cmd.get('output_file'))
return jsonify(rqtl_output)
def run_process(rscript_cmd, output_file, run_id):
"""Main function to do the streaming"""
# TODO: move this function to own file
# pylint: disable=consider-using-with
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})
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