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authorFrederick Muriuki Muriithi2022-07-28 10:19:54 +0300
committerFrederick Muriuki Muriithi2022-07-28 10:19:54 +0300
commit921b5fe752e4a947595a86572592d5bbdeb16ead (patch)
tree4d9a62be2bcadd2029f9d3cceb4c9e97373c7d33
parent3c8da2cae39efc25b320b78e2a1ed16afc1c5b8a (diff)
downloadgenenetwork3-921b5fe752e4a947595a86572592d5bbdeb16ead.tar.gz
Add command to run the sample correlations in an external process
-rw-r--r--gn3/api/correlation.py14
-rw-r--r--gn3/commands.py25
2 files changed, 31 insertions, 8 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 1667302..6e70899 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -9,13 +9,13 @@ from flask import request
from flask import current_app
from gn3.settings import SQL_URI
-from gn3.commands import run_async_cmd, compose_pcorrs_command
from gn3.db_utils import database_connector
+from gn3.commands import run_sample_corr_cmd
from gn3.responses.pcorrs_responses import build_response
+from gn3.commands import run_async_cmd, compose_pcorrs_command
from gn3.computations.correlations import map_shared_keys_to_values
from gn3.computations.correlations import compute_tissue_correlation
from gn3.computations.correlations import compute_all_lit_correlation
-from gn3.computations.correlations import compute_all_sample_correlation
correlation = Blueprint("correlation", __name__)
@@ -31,9 +31,8 @@ def compute_sample_integration(corr_method="pearson"):
this_trait_data = correlation_input.get("trait_data")
results = map_shared_keys_to_values(target_samplelist, target_data_values)
- correlation_results = compute_all_sample_correlation(corr_method=corr_method,
- this_trait=this_trait_data,
- target_dataset=results)
+ correlation_results = run_sample_corr_cmd(
+ corr_method, this_trait_data, results)
return jsonify(correlation_results)
@@ -50,9 +49,8 @@ def compute_sample_r(corr_method="pearson"):
this_trait_data = correlation_input.get("this_trait")
target_dataset_data = correlation_input.get("target_dataset")
- correlation_results = compute_all_sample_correlation(corr_method=corr_method,
- this_trait=this_trait_data,
- target_dataset=target_dataset_data)
+ correlation_results = run_sample_corr_cmd(
+ corr_method, this_trait_data, target_dataset_data)
return jsonify({
"corr_results": correlation_results
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)