diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/correlation.py | 14 | ||||
| -rw-r--r-- | gn3/commands.py | 25 |
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) |