refactor: import streaming functionality from module.

1 files changed, 1 insertions, 32 deletions

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 81bc5e4..f700afd 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -16,6 +16,7 @@ from gn3.computations.rqtl import (
     process_rqtl_pairscan,
     process_perm_output,
 )
+from gn3.computations.streaming import run_process
 from gn3.fs_helpers import assert_path_exists, get_tmpdir
 
 rqtl = Blueprint("rqtl", __name__)
@@ -102,35 +103,3 @@ def compute():
             rqtl_output["significant"],
         ) = process_perm_output(rqtl_cmd.get("output_file"))
     return jsonify(rqtl_output)
-
-
-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}