1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
|
"""module contains code to preprocess and call wgcna script"""
import os
import json
import uuid
import subprocess
import base64
from gn3.settings import TMPDIR
from gn3.commands import run_cmd
def dump_wgcna_data(request_data: dict):
"""function to dump request data to json file"""
filename = f"{str(uuid.uuid4())}.json"
temp_file_path = os.path.join(TMPDIR, filename)
request_data["TMPDIR"] = TMPDIR
with open(temp_file_path, "w", encoding="utf-8") 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"])
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"])
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_rscript_cmd(rscript_path: str, temp_file_path: str):
"""function to componse wgcna cmd"""
# (todo):issue relative paths to abs paths
cmd = f'"Rscript ./scripts/{rscript_path} {temp_file_path}"'
return cmd
def call_wgcna_script(rscript_path: str, request_data: dict):
"""function to call wgcna script"""
generated_file = dump_wgcna_data(request_data)
cmd = compose_rscript_cmd(rscript_path, generated_file)
# stream_cmd_output(request_data, cmd) disable streaming of data
try:
run_cmd_results = run_cmd(cmd)
with open(generated_file, "r", encoding="utf-8") as outputfile:
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": output_file_data,
**run_cmd_results
}
except FileNotFoundError:
# relook at handling errors gn3
return {
"output": "output file not found"
}
|
