From f73262a56745de17bdb582474e27726cb19bd95e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 5 Oct 2021 15:09:10 +0300
Subject: add function to process images

---
 gn3/computations/wgcna.py | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index 0fb56e8..26040d3 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -4,6 +4,7 @@ import os
 import json
 import uuid
 import subprocess
+import base64
 
 from gn3.settings import TMPDIR
 from gn3.commands import run_cmd
@@ -15,6 +16,8 @@ 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)
 
@@ -31,6 +34,16 @@ def stream_cmd_output(socket, cmd: str):
         line = line.decode("utf-8").rstrip()
 
 
+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
@@ -47,12 +60,18 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
 
         run_cmd_results = run_cmd(cmd)
 
+        print(run_cmd_results["output"])
+
         with open(generated_file, "r") as outputfile:
 
+            output_file_data = json.load(outputfile)
+            output_file_data["image_1"] = process_image(
+                output_file_data["output"]["imageLoc"])
+
             if run_cmd_results["code"] != 0:
                 return run_cmd_results
             return {
-                "data": json.load(outputfile),
+                "data": output_file_data,
                 **run_cmd_results
             }
     except FileNotFoundError:
-- 
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