From ed8ee3077211cc227089f87929a70ac8b7c4593f Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 22 Dec 2021 09:29:11 +0300
Subject: Add API endpoint for partial correlations

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* Add an API endpoint for the partial correlation.
* gn3/api/correlation.py:
---
 gn3/api/correlation.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'gn3/api')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index e936eaf..f84228a 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,4 +1,6 @@
 """Endpoints for running correlations"""
+import json
+
 from flask import jsonify
 from flask import Blueprint
 from flask import request
@@ -87,9 +89,20 @@ 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(
-- 
cgit 1.4.1


From c813dd68230a027b1b5acdbe9d3dba46f6bd1ad0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 22 Dec 2021 09:22:49 +0300
Subject: Encode the data to JSON and set the status code

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* Encode bytes objects to string
* Encode NaN values to "null"
* gn3/api/correlation.py:
---
 gn3/api/correlation.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index f84228a..c0b5806 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,9 +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
@@ -109,6 +109,8 @@ def partial_correlation():
         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),
+        400 if "error" in corr_results.keys() else 200)
+    response.headers["Content-Type"] = "application/json"
+    return response
-- 
cgit 1.4.1


From ac8528c5847f4a517c16b5283c06d3caeae8ef5e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 20 Dec 2021 07:19:16 +0300
Subject: Replace `NaN` with `null` in JSON string

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* `NaN` is not a valid JSON value, and leads to errors in the code. This
  commit replaces all `NaN` values with `null`.
---
 gn3/api/correlation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn3/api')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index c0b5806..1caf31f 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -110,7 +110,7 @@ def partial_correlation():
         tuple(trait_fullname(trait) for trait in args["control_traits"]),
         args["method"], int(args["criteria"]), args["target_db"])
     response = make_response(
-        json.dumps(corr_results, cls=OutputEncoder),
+        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
-- 
cgit 1.4.1