From 8854e3070f32bed95cb489eb36e7f258c02ec46e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 09:32:42 +0300
Subject: add initial endpoint for wgcna

---
 gn3/api/wgcna.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 gn3/api/wgcna.py

(limited to 'gn3/api')

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
new file mode 100644
index 0000000..a3bacdd
--- /dev/null
+++ b/gn3/api/wgcna.py
@@ -0,0 +1,13 @@
+"""endpoint to run wgcna analysis"""
+from flask import Blueprint
+from flask import request
+
+wgcna = Blueprint("wgcna", __name__)
+
+
+@wgcna.route("/run_wgcna", methods=["POST"])
+def run_wgcna():
+
+    _wgcna_data = request.json
+
+    return "success", 200
-- 
cgit v1.2.3


From f53a8a98206b4e8aedbf4b86e49f41ea140c9c6a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 14:02:13 +0300
Subject: pass user input to call script

---
 gn3/api/wgcna.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index a3bacdd..5d49493 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -1,13 +1,21 @@
 """endpoint to run wgcna analysis"""
 from flask import Blueprint
 from flask import request
+from flask import current_app
+
+from gn3.computations.wgcna import call_wgcna_script
 
 wgcna = Blueprint("wgcna", __name__)
 
 
 @wgcna.route("/run_wgcna", methods=["POST"])
 def run_wgcna():
+    """run wgcna:output should be a json with a the data"""
+
+    wgcna_data = request.json
+
+    wgcna_script = current_app.config["WGCNA_RSCRIPT"]
 
-    _wgcna_data = request.json
+    results = call_wgcna_script(wgcna_script, wgcna_data)
 
-    return "success", 200
+    return results, 200
-- 
cgit v1.2.3


From 6f7c60e6c438ada9a3b9032c8e4509351384e04f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 22 Sep 2021 00:49:22 +0300
Subject: jsonify results

---
 gn3/api/wgcna.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gn3/api')

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index 5d49493..89784c4 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -2,6 +2,7 @@
 from flask import Blueprint
 from flask import request
 from flask import current_app
+from flask import jsonify
 
 from gn3.computations.wgcna import call_wgcna_script
 
@@ -18,4 +19,4 @@ def run_wgcna():
 
     results = call_wgcna_script(wgcna_script, wgcna_data)
 
-    return results, 200
+    return jsonify(results), 200
-- 
cgit v1.2.3


From 62a5047be6cee5f692d44f97410cab11a01e3396 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 16:05:17 +0300
Subject: minor fixes for endpoint

---
 gn3/api/wgcna.py          | 3 +++
 gn3/computations/wgcna.py | 1 -
 2 files changed, 3 insertions(+), 1 deletion(-)

(limited to 'gn3/api')

diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index 89784c4..fa044cf 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -19,4 +19,7 @@ def run_wgcna():
 
     results = call_wgcna_script(wgcna_script, wgcna_data)
 
+    if results.get("data") is None:
+        return jsonify(results), 401
+
     return jsonify(results), 200
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index e9b76e8..436a888 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -44,6 +44,5 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
                 "data": json.load(outputfile),
                 **run_cmd_results
             }
-            # return json.load(outputfile)
     except Exception as error:
         raise error
-- 
cgit v1.2.3