diff options
| -rw-r--r-- | gn3/api/rqtl2.py | 30 |
1 files changed, 17 insertions, 13 deletions
diff --git a/gn3/api/rqtl2.py b/gn3/api/rqtl2.py index 8ac5ce3..ffa8755 100644 --- a/gn3/api/rqtl2.py +++ b/gn3/api/rqtl2.py @@ -13,8 +13,10 @@ 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") + # 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 = ( f"Rscript ./scripts/rqtl2_wrapper.R " @@ -28,30 +30,32 @@ def compute(): stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - # TODO rethink where we write this file for line in iter(process.stdout.readline, b""): - # dont modify + # these allow endpoint stream to read the file since + # no read and write file same tiem with open(output_file, "a+") 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"}) - else: - return jsonify({"msg": "fail", "error": "Process failed"}) + 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/<indetifier>", methods=["GET"]) -def stream(indetifier): +@rqtl2.route("/stream/<identifier>", methods=["GET"]) +def stream(identifier="output"): """ This endpoints streams stdout from a file expects the indetifier to be the file """ - # add seek position to this output_file = os.path.join(current_app.config.get("TMPDIR"), - f"{indetifier}.txt") + f"{identifier}.txt") seek_position = int(request.args.get("peak", 0)) with open(output_file) as file_handler: - # rethink how we do the read should this be stream / yield/peak ???? + # 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()}) |