diff options
Diffstat (limited to 'gn3/computations/wgcna.py')
| -rw-r--r-- | gn3/computations/wgcna.py | 28 |
1 files changed, 17 insertions, 11 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index d1d6d39..f7463c5 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -6,6 +6,7 @@ import uuid import subprocess import base64 + from gn3.settings import TMPDIR from gn3.commands import run_cmd @@ -24,22 +25,23 @@ def dump_wgcna_data(request_data: dict): return temp_file_path -def stream_cmd_output(socket, cmd: str): +def stream_cmd_output(request_data, cmd: str): """function to stream in realtime""" # xtodo syncing and closing /edge cases - socket.emit("output", {"data", f"calling you script {cmd}"}) - + 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) for line in iter(results.stdout.readline, b""): + line = line.decode("utf-8").rstrip() - socket.emit("output", - {"data": line}) - # wait for process to complete code + socketio.emit("output", + {"data": line}, namespace="/", room=request_data["socket_id"]) - socket.emit("output", {"data": "parsing the output results"}) + socketio.emit( + "output", {"data": "parsing the output results"}, namespace="/", room=request_data["socket_id"]) def process_image(image_loc: str) -> bytes: @@ -64,9 +66,11 @@ def call_wgcna_script(rscript_path: str, request_data: dict): generated_file = dump_wgcna_data(request_data) cmd = compose_wgcna_cmd(rscript_path, generated_file) + stream_cmd_output(request_data, cmd) + try: - run_cmd_results = run_cmd(cmd) + # run_cmd_results = run_cmd(cmd) with open(generated_file, "r") as outputfile: @@ -74,12 +78,14 @@ def call_wgcna_script(rscript_path: str, request_data: dict): # json format only supports unicode string// to get image data reconvert output_file_data["output"]["image_data"] = process_image( output_file_data["output"]["imageLoc"]).decode("ascii") + output_file_data["output"]["image_data2"] = process_image( + output_file_data["output"]["heatMap"]).decode("ascii") - if run_cmd_results["code"] != 0: - return run_cmd_results + # if run_cmd_results["code"] != 0: + # return run_cmd_results return { "data": output_file_data, - **run_cmd_results + "output": "" } except FileNotFoundError: # relook at handling errors gn3 |