Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations

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: