Merge pull request #590 from Alexanderlacuna/bugfix/rpy2-tissue-broken-links

replace rpy2  for tissue correlation

4 files changed, 36 insertions, 33 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 bebef9e7..e936f28c 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -25,6 +25,7 @@ from base.data_set import create_dataset
 
 from utility import hmac
 
+
 def set_template_vars(start_vars, correlation_data):
     corr_type = start_vars['corr_type']
     corr_method = start_vars['corr_sample_method']
@@ -55,11 +56,14 @@ def set_template_vars(start_vars, correlation_data):
 
     correlation_data['corr_method'] = corr_method
     correlation_data['filter_cols'] = filter_cols
-    correlation_data['header_fields'] = get_header_fields(target_dataset_ob.type, correlation_data['corr_method'])
-    correlation_data['formatted_corr_type'] = get_formatted_corr_type(corr_type, corr_method)
+    correlation_data['header_fields'] = get_header_fields(
+        target_dataset_ob.type, correlation_data['corr_method'])
+    correlation_data['formatted_corr_type'] = get_formatted_corr_type(
+        corr_type, corr_method)
 
     return correlation_data
 
+
 def correlation_json_for_table(correlation_data, this_trait, this_dataset, target_dataset_ob):
     """Return JSON data for use with the DataTable in the correlation result page
 
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 12dddf89..049ebe6d 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -208,7 +208,7 @@
                     <a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a>
             </p>
             <p>
-            Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <span class="broken_link" href="https://webchat.freenode.net/">IRC</span> (#genenetwork channel).
+            Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <span class="broken_link" href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</span> and find us on <a href="https://webchat.freenode.net#genenetwork">IRC</a> (#genenetwork channel).
             {% if version: %}
             <p><small>GeneNetwork {{ version }}</small></p>
             {% endif %}