diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/correlation.py | 21 |
1 files changed, 18 insertions, 3 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index e936eaf..1caf31f 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -1,7 +1,9 @@ """Endpoints for running correlations""" +import json from flask import jsonify from flask import Blueprint from flask import request +from flask import make_response from gn3.computations.correlations import compute_all_sample_correlation from gn3.computations.correlations import compute_all_lit_correlation @@ -87,15 +89,28 @@ def compute_tissue_corr(corr_method="pearson"): @correlation.route("/partial", methods=["POST"]) def partial_correlation(): + """API endpoint for partial correlations.""" def trait_fullname(trait): return f"{trait['dataset']}::{trait['name']}" + 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, obj): + if isinstance(obj, bytes): + return str(obj, encoding="utf-8") + return json.JSONEncoder.default(self, obj) + args = request.get_json() 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["criteria"]), args["target_db"]) - return make_response( - jsonify(corr_results), - 400) + response = make_response( + json.dumps(corr_results, cls=OutputEncoder).replace(": NaN", ": null"), + 400 if "error" in corr_results.keys() else 200) + response.headers["Content-Type"] = "application/json" + return response |