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authorFrederick Muriuki Muriithi2021-10-25 15:13:05 +0300
committerFrederick Muriuki Muriithi2021-10-25 15:13:05 +0300
commit5a472ebab04c68cd5228f253cc98d0ae22a520d7 (patch)
tree3d6b1a5a8933896a6e7fdc98f473ef069accd348 /gn3
parent0814eea6b57e45d4337424e63c164d204d03b64d (diff)
parent5440bfcd6940db08c4479a39ba66dbc802b2c426 (diff)
downloadgenenetwork3-5a472ebab04c68cd5228f253cc98d0ae22a520d7.tar.gz
Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/wgcna.py49
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: