1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
|
""" 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,
prepare_files,
validate_required_keys,
write_input_file,
process_qtl2_results
)
from gn3.computations.streaming import run_process
from gn3.computations.streaming import enable_streaming
rqtl2 = Blueprint("rqtl2", __name__)
@rqtl2.route("/compute", methods=["POST"])
@enable_streaming
def compute(log_file):
"""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 "physical_map_data" not in data and "geno_map_data" not in data:
return jsonify(error="You need to Provide\
Either the Physical map or Geno Map data of markers"), 400
run_id = request.args.get("id", "output")
# prepare necessary files and dir for computation
(workspace_dir, input_file,
output_file, _log2_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)
rqtl_path = Path(current_app.root_path) / "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:
# Err out for any non-zero status code
return jsonify(process_output), 400
results = process_qtl2_results(output_file)
shutil.rmtree(workspace_dir, ignore_errors=True, onerror=None)
return jsonify(results)
|
