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authorFrederick Muriuki Muriithi2022-02-23 14:51:47 +0300
committerFrederick Muriuki Muriithi2022-03-03 10:20:04 +0300
commit6d39c92fbc9a7b82cd8eef60c62cd5d83acb49a1 (patch)
tree7efab53cc8fc367f433ac01ece95b0fbecc858d9 /gn3/api
parent8e0fcfa78fcdb5bdd5b49e2b1ac918ae9cc0fc53 (diff)
downloadgenenetwork3-6d39c92fbc9a7b82cd8eef60c62cd5d83acb49a1.tar.gz
Run partial correlations in an external process
Run the partial correlations code in an external python process decoupling it from the server and making it asynchronous. Summary of changes: * gn3/api/correlation.py: - Remove response processing code - Queue partial corrs processing - Create new endpoint to get results * gn3/commands.py - Compose the pcorrs command to be run in an external process - Enable running of subprocess commands with list args * gn3/responses/__init__.py: new module indicator file * gn3/responses/pcorrs_responses.py: Hold response processing code extracted from ~gn3.api.correlations.py~ file * scripts/partial_correlations.py: CLI script to process the pcorrs * sheepdog/worker.py: - Add the *genenetwork3* path at the beginning of the ~sys.path~ list to override any GN3 in the site-packages - Add any environment variables to be set for the command to be run
Diffstat (limited to 'gn3/api')
-rw-r--r--gn3/api/correlation.py65
1 files changed, 31 insertions, 34 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 00b3ad5..14c029c 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,17 +1,22 @@
"""Endpoints for running correlations"""
+import sys
import json
from functools import reduce
+import redis
from flask import jsonify
from flask import Blueprint
from flask import request
-from flask import make_response
+from flask import current_app
-from gn3.computations.correlations import compute_all_sample_correlation
-from gn3.computations.correlations import compute_all_lit_correlation
-from gn3.computations.correlations import compute_tissue_correlation
-from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.settings import SQL_URI
+from gn3.commands import queue_cmd, compose_pcorrs_command
from gn3.db_utils import database_connector
+from gn3.responses.pcorrs_responses import build_response
+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
from gn3.computations.partial_correlations import partial_correlations_entry
correlation = Blueprint("correlation", __name__)
@@ -93,7 +98,7 @@ def compute_tissue_corr(corr_method="pearson"):
def partial_correlation():
"""API endpoint for partial correlations."""
def trait_fullname(trait):
- return f"{trait['dataset']}::{trait['name']}"
+ return f"{trait['dataset']}::{trait['trait_name']}"
def __field_errors__(args):
def __check__(acc, field):
@@ -107,37 +112,29 @@ def partial_correlation():
if request_data is None:
return ("No request data",)
- return reduce(__field_errors__(args), fields, errors)
-
- class OutputEncoder(json.JSONEncoder):
- """
- Class to encode output into JSON, for objects which the default
- json.JSONEncoder class does not have default encoding for.
- """
- def default(self, o):
- if isinstance(o, bytes):
- return str(o, encoding="utf-8")
- return json.JSONEncoder.default(self, o)
-
- def __build_response__(data):
- status_codes = {"error": 400, "not-found": 404, "success": 200}
- response = make_response(
- json.dumps(data, cls=OutputEncoder),
- status_codes[data["status"]])
- response.headers["Content-Type"] = "application/json"
- return response
-
- args = request.get_json()
+ return reduce(__field_errors__(request_data), fields, errors)
+
+ args = json.loads(request.get_json())
request_errors = __errors__(
args, ("primary_trait", "control_traits", "target_db", "method"))
if request_errors:
- return __build_response__({
+ return build_response({
"status": "error",
"messages": request_errors,
"error_type": "Client Error"})
- conn, _cursor_object = database_connector()
- corr_results = partial_correlations_entry(
- conn, trait_fullname(args["primary_trait"]),
- tuple(trait_fullname(trait) for trait in args["control_traits"]),
- args["method"], int(args.get("criteria", 500)), args["target_db"])
- return __build_response__(corr_results)
+ return build_response({
+ "status": "success",
+ "results": queue_cmd(
+ conn=redis.Redis(),
+ cmd=compose_pcorrs_command(
+ trait_fullname(args["primary_trait"]),
+ tuple(
+ trait_fullname(trait) for trait in args["control_traits"]),
+ args["method"], args["target_db"],
+ int(args.get("criteria", 500))),
+ job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+ env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})})
+
+@correlation.route("/partial/<job_id>", methods=["GET"])
+def partial_correlation_results():
+ raise Exception("Not implemented!!")