diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/correlation.py | 65 |
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!!") |