diff options
Diffstat (limited to 'gn3/computations/wgcna.py')
| -rw-r--r-- | gn3/computations/wgcna.py | 28 |
1 files changed, 13 insertions, 15 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index ab12fe7..c985491 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -19,7 +19,7 @@ def dump_wgcna_data(request_data: dict): request_data["TMPDIR"] = TMPDIR - with open(temp_file_path, "w") as output_file: + with open(temp_file_path, "w", encoding="utf-8") as output_file: json.dump(request_data, output_file) return temp_file_path @@ -31,20 +31,18 @@ def stream_cmd_output(socketio, request_data, cmd: str): socketio.emit("output", {"data": f"calling you script {cmd}"}, namespace="/", room=request_data["socket_id"]) - results = subprocess.Popen( - cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) + with subprocess.Popen( + cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) as results: + if results.stdout is not None: + for line in iter(results.stdout.readline, b""): + socketio.emit("output", + {"data": line.decode("utf-8").rstrip()}, + namespace="/", room=request_data["socket_id"]) - if results.stdout is not None: - - for line in iter(results.stdout.readline, b""): - socketio.emit("output", - {"data": line.decode("utf-8").rstrip()}, - namespace="/", room=request_data["socket_id"]) - - socketio.emit( - "output", {"data": - "parsing the output results"}, namespace="/", - room=request_data["socket_id"]) + socketio.emit( + "output", {"data": + "parsing the output results"}, namespace="/", + room=request_data["socket_id"]) def process_image(image_loc: str) -> bytes: @@ -75,7 +73,7 @@ def call_wgcna_script(rscript_path: str, request_data: dict): run_cmd_results = run_cmd(cmd) - with open(generated_file, "r") as outputfile: + with open(generated_file, "r", encoding="utf-8") as outputfile: if run_cmd_results["code"] != 0: return run_cmd_results |