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-rw-r--r--gn3/commands.py25
1 files changed, 25 insertions, 0 deletions
diff --git a/gn3/commands.py b/gn3/commands.py
index 0b8db5b..d45d9e8 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -2,6 +2,8 @@
commands"""
import sys
import json
+import pickle
+import tempfile
import subprocess
from datetime import datetime
@@ -14,6 +16,7 @@ from typing import Sequence
from uuid import uuid4
from redis.client import Redis # Used only in type hinting
+from gn3.random import random_string
from gn3.exceptions import RedisConnectionError
@@ -120,6 +123,28 @@ Returns the name of the specific redis hash for the specific task.
conn.hset(name=unique_id, key="env", value=json.dumps(env))
return unique_id
+def run_sample_corr_cmd(method, this_trait_data, target_dataset_data):
+ "Run the sample correlations in an external process, returning the results."
+ with tempfile.TemporaryDirectory() as tempdir:
+ traitfile = f"{tempdir}/traitfile_{random_string(10)}"
+ targetfile = f"{tempdir}/targetdb_{random_string(10)}"
+ destfile = f"{tempdir}/corrs_{random_string(10)}"
+ with open(traitfile, "wb") as trtfl:
+ pickle.dump(this_trait_data, trtfl)
+
+ with open(targetfile, "wb") as targfl:
+ pickle.dump(target_dataset_data, targfl)
+
+ subprocess.run(
+ ["python3", "-m", "scripts.sample_correlations", method,
+ traitfile, targetfile, destfile],
+ check=True)
+
+ with open(destfile, "rb") as dstfl:
+ correlation_results = pickle.load(dstfl)
+
+ return correlation_results
+
def run_cmd(cmd: str, success_codes: Tuple = (0,), env: str = None) -> Dict:
"""Run CMD and return the CMD's status code and output as a dict"""
parsed_cmd = json.loads(cmd)