1 files changed, 54 insertions, 0 deletions
diff --git a/gn3/computations/streaming.py b/gn3/computations/streaming.py
new file mode 100644
index 0000000..b5afb5b
--- /dev/null
+++ b/gn3/computations/streaming.py
@@ -0,0 +1,54 @@
+"""Module contains streaming procedures  for genenetwork. """
+import os
+import subprocess
+from functools import wraps
+from flask import current_app, request
+
+
+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 for 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 each 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}
+
+
+def enable_streaming(func):
+    """Decorator function to enable streaming for an endpoint
+    Note: should only be used  in an app context
+    """
+    @wraps(func)
+    def decorated_function(*args, **kwargs):
+        run_id = request.args.get("id")
+        stream_output_file = os.path.join(current_app.config.get("TMPDIR"),
+                                          f"{run_id}.txt")
+        with open(stream_output_file, "w+", encoding="utf-8",
+                  ) as file_handler:
+            file_handler.write("File created for streaming\n"
+                               )
+        return func(stream_output_file, *args, **kwargs)
+    return decorated_function