diff options
| -rw-r--r-- | gn3/api/rqtl2.py | 74 |
1 files changed, 38 insertions, 36 deletions
diff --git a/gn3/api/rqtl2.py b/gn3/api/rqtl2.py index e26b9ed..dbbb536 100644 --- a/gn3/api/rqtl2.py +++ b/gn3/api/rqtl2.py @@ -1,47 +1,49 @@ """ File contains endpoints for rqlt2""" - -import subprocess -import os +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.streaming import run_process rqtl2 = Blueprint("rqtl2", __name__) -@rqtl2.route("/compute", methods=["GET"]) +@rqtl2.route("/compute", methods=["POST"]) def compute(): """Endpoint for computing QTL analysis using R/QTL2""" - # get the run id to act as file identifier default to output + data = request.json + # main requirements for creating the cross + 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 + # Users should provide atleast the one of this + 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") - 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" - ) - # 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}) + # 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) + # check if the rscript cmd command exist + 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) + # run the rscript in as a subprocess which capture stdout in the log file + process_output = run_process(rqtl2_cmd.split(),log_file, run_id) + if process_output["code"]!=0: + return jsonify(process_output), 400 + # TODO: process the results and return results to gn2 + # rm the workspace directory + shutil.rmtree(workspace_dir, ignore_errors=True, onerror=None) + return process_output |