From 43d1bb7f6cd2b5890d5b3eb7c357caafda25a35c Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 16 Mar 2021 10:36:58 +0300
Subject: Refactor/clean up correlations (#4)

* initial commit for Refactor/clean-up-correlation

* add python scipy dependency

* initial commit for sample correlation

* initial commit for sample correlation endpoint

* initial commit for integration and unittest

* initial commit for registering  correlation blueprint

* add and modify unittest and integration tests for correlation

* Add compute compute_all_sample_corr   method for correlation

* add scipy to requirement txt file

* add tissue correlation for trait list

* add unittest for tissue correlation

* add lit correlation for trait list

* add unittests for lit correlation for trait list

* modify lit correlarion for trait list

* add unittests for lit correlation for trait list

* add correlation metho  in dynamic url

* add file format for expected structure input  while doing sample correlation

* modify input data structure -> add  trait id

* update tests for sample r correlation

* add compute all lit correlation method

* add endpoint for computing lit_corr

* add unit and integration tests for computing lit corr

* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation

* add unittest and integration tests for tissue correlation

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>---
 gn3/api/correlation.py | 77 +++++++++++++++++++++++++++++++-------------------
 1 file changed, 48 insertions(+), 29 deletions(-)

(limited to 'gn3/api/correlation.py')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 217b7ce..56b8381 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,44 +1,63 @@
-"""Endpoints for computing correlation"""
-import time
-from flask import Blueprint
+"""Endpoints for running correlations"""
+from unittest import mock
+
 from flask import jsonify
+from flask import Blueprint
 from flask import request
-from flask import g
-from sqlalchemy import create_engine
 
-from default_settings import SQL_URI
-from gn3.correlation.correlation_computations import compute_correlation
+from gn3.computations.correlations import compute_all_sample_correlation
+from gn3.computations.correlations import compute_all_lit_correlation
+from gn3.computations.correlations import compute_all_tissue_correlation
+
 
 correlation = Blueprint("correlation", __name__)
 
 
-# xtodo implement neat db setup
-@correlation.before_request
-def connect_db():
-    """add connection to db method"""
-    print("@app.before_request connect_db")
-    db_connection = getattr(g, '_database', None)
-    if db_connection is None:
-        print("Get new database connector")
-        g.db = g._database = create_engine(SQL_URI, encoding="latin1")
+@correlation.route("/sample_r/<string:corr_method>", methods=["POST"])
+def compute_sample_r(corr_method="pearson"):
+    """correlation endpoint for computing sample r correlations\
+    api expects the trait data with has the trait and also the\
+    target_dataset  data"""
+    correlation_input = request.get_json()
+
+    # xtodo move code below to compute_all_sampl correlation
+    this_trait_data = correlation_input.get("this_trait")
+    target_datasets = correlation_input.get("target_dataset")
+
+    correlation_results = compute_all_sample_correlation(corr_method=corr_method,
+                                                         this_trait=this_trait_data,
+                                                         target_dataset=target_datasets)
+
+    return jsonify({
+        "corr_results": correlation_results
+    })
+
 
-    g.initial_time = time.time()
+@correlation.route("/lit_corr/<string:species>/<int:gene_id>", methods=["POST"])
+def compute_lit_corr(species=None, gene_id=None):
+    """api endpoint for doing lit correlation.results for lit correlation\
+    are fetched from the database this is the only case where the db\
+    might be needed for actual computing of the correlation results"""
 
+    database_instance = mock.Mock()
+    target_traits_gene_ids = request.get_json()
 
-@correlation.route("/corr_compute", methods=["POST"])
-def corr_compute_page():
-    """api for doing  correlation"""
+    lit_corr_results = compute_all_lit_correlation(
+        database_instance=database_instance, trait_lists=target_traits_gene_ids,
+        species=species, gene_id=gene_id)
 
-    correlation_input = request.json
+    return jsonify(lit_corr_results)
 
-    if correlation_input is None:
-        return jsonify({"error": str("Bad request")}), 400
 
-    try:
-        corr_results = compute_correlation(
-            correlation_input_data=correlation_input)
+@correlation.route("/tissue_corr/<string:corr_method>", methods=["POST"])
+def compute_tissue_corr(corr_method="pearson"):
+    """api endpoint fr doing tissue correlation"""
+    tissue_input_data = request.get_json()
+    primary_tissue_dict = tissue_input_data["primary_tissue"]
+    target_tissues_dict_list = tissue_input_data["target_tissues"]
 
-    except Exception as error:  # pylint: disable=broad-except
-        return jsonify({"error": str(error)})
+    results = compute_all_tissue_correlation(primary_tissue_dict=primary_tissue_dict,
+                                             target_tissues_dict_list=target_tissues_dict_list,
+                                             corr_method=corr_method)
 
-    return {"correlation_results": corr_results}
+    return jsonify(results)
\ No newline at end of file
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