Merge pull request #481 from Alexanderlacuna/test-SampleList

Test sample list

3 files changed, 60 insertions, 4 deletions

diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py
new file mode 100644
index 00000000..34c51e3e
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/testSampleList.py
@@ -0,0 +1,16 @@
+import unittest
+import re
+from unittest import mock
+from wqflask.show_trait.SampleList import natural_sort
+
+
+class TestSampleList(unittest.TestCase):
+    def test_natural_sort(self):
+        "Sort the list into natural alphanumeric order."
+
+        characters_list = ["z", "f", "q", "s", "t", "a", "g"]
+        names_list = ["temp1", "publish", "Sample", "Dataset"]
+        sorted_list_a=natural_sort(characters_list)
+        sorted_list_b=natural_sort(names_list)
+        self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"])
+        self.assertEqual(sorted_list_b,["Dataset", "Sample", "publish", "temp1"])
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 24150738..8c866874 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -11,6 +11,7 @@ from wqflask.show_trait.show_trait import get_trait_units
 from wqflask.show_trait.show_trait import get_nearest_marker
 from wqflask.show_trait.show_trait import get_genotype_scales
 from wqflask.show_trait.show_trait import requests
+from wqflask.show_trait.show_trait import get_scales_from_genofile
 
 
 class TraitObject:
@@ -240,3 +241,38 @@ class TestTraits(unittest.TestCase):
         expected_results = {f"{file_location}": [["physic", "Mb"]]}
         self.assertEqual(get_genotype_scales(file_location), expected_results)
         mock_get_scales.assert_called_once_with(file_location)
+
+
+    @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
+    def test_get_scales_from_genofile_found(self, mock_ignore_location):
+        """"add test for get scales from genofile where file is found"""
+        mock_ignore_location.return_value = True
+        geno_file = """
+                #sample line    with no  @scales:other\n
+                #sample line     @scales and :separated   by semicolon\n
+                This attempts    to check whether\n
+                """
+
+        geno_file_string = "@line start with  @ and has @scale:morgan"
+
+        file_location = "~/data/file.geno"
+
+        mock_open_geno_file = mock.mock_open(read_data=geno_file)
+        with mock.patch("builtins.open", mock_open_geno_file):
+            results = get_scales_from_genofile(file_location)
+            self.assertEqual(results, [["morgan", "cM"]])
+
+        mock_open_string = mock.mock_open(read_data=geno_file_string)
+
+        with mock.patch("builtins.open", mock_open_string):
+            result2 = get_scales_from_genofile(file_location)
+            self.assertEqual([['morgan', 'cM']], result2)
+
+    @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
+    def test_get_scales_from_genofile_not_found(self, mock_location_ignore):
+        mock_location_ignore.return_value = False
+
+        expected_results = [["physic", "Mb"]]
+        results = get_scales_from_genofile("~/data/file")
+        mock_location_ignore.assert_called_once_with("~/data/file", "genotype")
+        self.assertEqual(results, expected_results)
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index a535c493..00495377 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -8,6 +8,7 @@ from pprint import pformat as pf
 from utility import Plot
 from utility import Bunch
 
+
 class SampleList(object):
     def __init__(self,
                  dataset,
@@ -72,7 +73,8 @@ class SampleList(object):
             self.sample_list.append(sample)
 
         self.se_exists = any(sample.variance for sample in self.sample_list)
-        self.num_cases_exists = any(sample.num_cases for sample in self.sample_list)
+        self.num_cases_exists = any(
+            sample.num_cases for sample in self.sample_list)
 
         first_attr_col = self.get_first_attr_col()
         for sample in self.sample_list:
@@ -115,7 +117,7 @@ class SampleList(object):
             self.attributes[key].name = name
             self.attributes[key].distinct_values = [
                 item.Value for item in values]
-            natural_sort(self.attributes[key].distinct_values)
+            self.attributes[key].distinct_values=natural_sort(self.attributes[key].distinct_values)
             all_numbers = True
             for value in self.attributes[key].distinct_values:
                 try:
@@ -167,7 +169,8 @@ class SampleList(object):
 
         return first_attr_col
 
-def natural_sort(list, key=lambda s: s):
+
+def natural_sort(a_list, key=lambda s: s):
     """
     Sort the list into natural alphanumeric order.
     """
@@ -175,4 +178,5 @@ def natural_sort(list, key=lambda s: s):
         def convert(text): return int(text) if text.isdigit() else text
         return lambda s: [convert(c) for c in re.split('([0-9]+)', key(s))]
     sort_key = get_alphanum_key_func(key)
-    list.sort(key=sort_key)
\ No newline at end of file
+    sorted_list = sorted(a_list, key=sort_key)
+    return sorted_list