replace rpy2 for tissue corr

3 files changed, 30 insertions, 32 deletions

diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index 2bbeab1f..a8cf6006 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -1,10 +1,30 @@
+"""module contains tests for correlation functions"""
+
 import unittest
 from unittest import mock
+
 from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
 from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
 
 
 class TestCorrelationFunctions(unittest.TestCase):
+    """test for correlation helper functions"""
+
+    @mock.patch("wqflask.correlation.correlation_functions.compute_corr_coeff_p_value")
+    def test_tissue_corr_computation(self, mock_tiss_corr_computation):
+        """test for cal_zero_order_corr_for_tiss"""
+
+        primary_values = [9.288, 9.313, 8.988, 9.660, 8.21]
+        target_values = [9.586, 8.498, 9.362, 8.820, 8.786]
+
+        mock_tiss_corr_computation.return_value = (0.51, 0.7)
+
+        results = cal_zero_order_corr_for_tiss(primary_values, target_values)
+        mock_tiss_corr_computation.assert_called_once_with(
+            primary_values=primary_values, target_values=target_values,
+            corr_method="pearson")
+
+        self.assertEqual(len(results), 3)
 
     @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
     def test_get_trait_symbol_and_tissue_values(self, mock_class):
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index c8b9da0e..85b25d60 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -21,15 +21,10 @@
 # This module is used by GeneNetwork project (www.genenetwork.org)
 #
 # Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by NL 2011/03/23
 
-import math
-import string
 
 from base.mrna_assay_tissue_data import MrnaAssayTissueData
-
-from flask import Flask, g
+from gn3.computations.correlations import compute_corr_coeff_p_value
 
 
 #####################################################################################
@@ -45,31 +40,14 @@ from flask import Flask, g
 # the same tissue order
 #####################################################################################
 
-def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearson'):
-
-    N = len(primaryValue)
-    # R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue))))
-    # for i in range(len(primaryValue)):
-    #     R_primary[i] = primaryValue[i]
 
-    # R_target = rpy2.robjects.FloatVector(list(range(len(targetValue))))
-    # for i in range(len(targetValue)):
-    #     R_target[i] = targetValue[i]
+def cal_zero_order_corr_for_tiss(primary_values, target_values, method="pearson"):
+    """function use calls gn3 to compute corr,p_val"""
 
-    # R_corr_test = rpy2.robjects.r['cor.test']
-    # if method == 'spearman':
-    #     R_result = R_corr_test(R_primary, R_target, method='spearman')
-    # else:
-    #     R_result = R_corr_test(R_primary, R_target)
-
-    # corr_result = []
-    # corr_result.append(R_result[3][0])
-    # corr_result.append(N)
-    # corr_result.append(R_result[2][0])
-
-    return [None, N, None]
-    # return corr_result
+    (corr_coeff, p_val) = compute_corr_coeff_p_value(
+        primary_values=primary_values, target_values=target_values, corr_method=method)
 
+    return (corr_coeff, len(primary_values), p_val)
 
 ########################################################################################################
 # input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
@@ -80,8 +58,9 @@ def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearso
 #          then call getSymbolValuePairDict function and merge the results.
 ########################################################################################################
 
+
 def get_trait_symbol_and_tissue_values(symbol_list=None):
     tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
-    if len(tissue_data.gene_symbols) >0:
+    if len(tissue_data.gene_symbols) > 0:
         results = tissue_data.get_symbol_values_pairs()
-        return results 
+        return results
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index f1cf3733..b0496bfe 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -34,6 +34,7 @@ from utility import corr_result_helpers
 from utility import hmac
 
 from wqflask.correlation import correlation_functions
+
 from utility.benchmark import Bench
 
 from utility.type_checking import is_str
@@ -93,7 +94,6 @@ class CorrelationResults:
             self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
             self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
 
-
             if ('loc_chr' in start_vars
                 and 'min_loc_mb' in start_vars
                     and 'max_loc_mb' in start_vars):
@@ -198,7 +198,6 @@ class CorrelationResults:
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
-
                 if (float(self.correlation_data[trait][0]) >= self.p_range_lower
                         and float(self.correlation_data[trait][0]) <= self.p_range_upper):