diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/wgcna.py | 49 |
1 files changed, 47 insertions, 2 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index fd508fa..ab12fe7 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -3,8 +3,11 @@ import os import json import uuid -from gn3.settings import TMPDIR +import subprocess +import base64 + +from gn3.settings import TMPDIR from gn3.commands import run_cmd @@ -14,12 +17,46 @@ def dump_wgcna_data(request_data: dict): temp_file_path = os.path.join(TMPDIR, filename) + request_data["TMPDIR"] = TMPDIR + with open(temp_file_path, "w") as output_file: json.dump(request_data, output_file) return temp_file_path +def stream_cmd_output(socketio, request_data, cmd: str): + """function to stream in realtime""" + # xtodo syncing and closing /edge cases + + 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) + + 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"]) + + +def process_image(image_loc: str) -> bytes: + """encode the image""" + + try: + with open(image_loc, "rb") as image_file: + return base64.b64encode(image_file.read()) + except FileNotFoundError: + return b"" + + def compose_wgcna_cmd(rscript_path: str, temp_file_path: str): """function to componse wgcna cmd""" # (todo):issue relative paths to abs paths @@ -32,6 +69,8 @@ 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) disable streaming of data + try: run_cmd_results = run_cmd(cmd) @@ -40,8 +79,14 @@ def call_wgcna_script(rscript_path: str, request_data: dict): if run_cmd_results["code"] != 0: return run_cmd_results + + output_file_data = json.load(outputfile) + output_file_data["output"]["image_data"] = process_image( + output_file_data["output"]["imageLoc"]).decode("ascii") + # json format only supports unicode string// to get image data reconvert + return { - "data": json.load(outputfile), + "data": output_file_data, **run_cmd_results } except FileNotFoundError: |