feat: Add function to run an external process and capture result in a file.

1 files changed, 34 insertions, 2 deletions

diff --git a/gn3/computations/streaming.py b/gn3/computations/streaming.py
index 7155adb..d39aa7f 100644
--- a/gn3/computations/streaming.py
+++ b/gn3/computations/streaming.py
@@ -1,2 +1,34 @@
-""" Module contains streaming functionality for genenetwork
-"""
+"""Module contains streaming procedures  for genenetwork. """
+import subprocess
+
+
+def run_process(cmd, output_file, run_id):
+    """Function to execute an external process and
+       capture the stdout in a file
+      input:
+           cmd: the command to execute as a list of args.
+           output_file: abs file path to write the stdout.
+           run_id: unique id to identify the process
+
+      output:
+          Dict with the results o either success or failure.
+    """
+    try:
+        # phase: execute the  rscript cmd
+        with subprocess.Popen(
+            cmd,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+        ) as process:
+            for line in iter(process.stdout.readline, b""):
+                # phase: capture the stdout for eaching line allowing read and write
+                with open(output_file, "a+", encoding="utf-8") as file_handler:
+                    file_handler.write(line.decode("utf-8"))
+            process.wait()
+        if process.returncode == 0:
+            return {"msg": "success", "code": 0, "run_id": run_id}
+        return {"msg": "error occurred", "error": "Process failed",
+                "code": process.returncode, "run_id": run_id}
+    except subprocess.CalledProcessError as error:
+        return {"msg": "error occurred",
+                "error": str(error), "run_id": run_id}