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"""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") as output_file:
json.dump(request_data, output_file)
return temp_file_path
def stream_cmd_output(socket, cmd: str):
"""function to stream in realtime"""
# xtodo syncing and closing /edge cases
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()
# xtodo emit the data
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 as e:
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
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_wgcna_cmd(rscript_path, generated_file)
try:
run_cmd_results = run_cmd(cmd)
print(run_cmd_results["output"])
with open(generated_file, "r") as outputfile:
output_file_data = json.load(outputfile)
# 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")
if run_cmd_results["code"] != 0:
return run_cmd_results
return {
"data": output_file_data,
**run_cmd_results
}
except FileNotFoundError:
# relook at handling errors gn3
return {
"output": "output file not found"
}
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