30 files changed, 127 insertions, 1 deletions
diff --git a/wqflask/tests/base/__init__.py b/wqflask/tests/integration/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/base/__init__.py
+++ b/wqflask/tests/integration/__init__.py
diff --git a/wqflask/tests/integration/test_markdown_routes.py b/wqflask/tests/integration/test_markdown_routes.py
new file mode 100644
index 00000000..5e3e5045
--- /dev/null
+++ b/wqflask/tests/integration/test_markdown_routes.py
@@ -0,0 +1,21 @@
+"Integration tests for markdown routes"
+import unittest
+
+from bs4 import BeautifulSoup
+
+from wqflask import app
+
+
+class TestGenMenu(unittest.TestCase):
+    """Tests for glossary"""
+
+    def setUp(self):
+        self.app = app.test_client()
+
+    def tearDown(self):
+        pass
+
+    def test_glossary_page(self):
+        """Test that the glossary page is rendered properly"""
+        response = self.app.get('/glossary', follow_redirects=True)
+        pass
diff --git a/wqflask/tests/utility/__init__.py b/wqflask/tests/unit/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/utility/__init__.py
+++ b/wqflask/tests/unit/__init__.py
diff --git a/wqflask/tests/wqflask/__init__.py b/wqflask/tests/unit/base/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/__init__.py
+++ b/wqflask/tests/unit/base/__init__.py
diff --git a/wqflask/tests/base/data.py b/wqflask/tests/unit/base/data.py
index 06a5a989..06a5a989 100644
--- a/wqflask/tests/base/data.py
+++ b/wqflask/tests/unit/base/data.py
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index 96563a16..96563a16 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/unit/base/test_general_object.py
index 00fd3c72..00fd3c72 100644
--- a/wqflask/tests/base/test_general_object.py
+++ b/wqflask/tests/unit/base/test_general_object.py
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
index 826ccefd..826ccefd 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/unit/base/test_trait.py
diff --git a/wqflask/tests/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..8e8ba482 100644
--- a/wqflask/tests/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
diff --git a/wqflask/tests/wqflask/api/__init__.py b/wqflask/tests/unit/utility/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/api/__init__.py
+++ b/wqflask/tests/unit/utility/__init__.py
diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index 5c391be5..5c391be5 100644
--- a/wqflask/tests/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
diff --git a/wqflask/tests/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..8d90a1ec 100644
--- a/wqflask/tests/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
diff --git a/wqflask/tests/utility/test_corestats.py b/wqflask/tests/unit/utility/test_corestats.py
index cf91a248..cf91a248 100644
--- a/wqflask/tests/utility/test_corestats.py
+++ b/wqflask/tests/unit/utility/test_corestats.py
diff --git a/wqflask/tests/utility/test_corr_result_helpers.py b/wqflask/tests/unit/utility/test_corr_result_helpers.py
index e196fbdf..e196fbdf 100644
--- a/wqflask/tests/utility/test_corr_result_helpers.py
+++ b/wqflask/tests/unit/utility/test_corr_result_helpers.py
diff --git a/wqflask/tests/utility/test_formatting.py b/wqflask/tests/unit/utility/test_formatting.py
index 9d3033d1..9d3033d1 100644
--- a/wqflask/tests/utility/test_formatting.py
+++ b/wqflask/tests/unit/utility/test_formatting.py
diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/unit/utility/test_hmac.py
index 4e3652f8..13d6261d 100644
--- a/wqflask/tests/utility/test_hmac.py
+++ b/wqflask/tests/unit/utility/test_hmac.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Test hmac utility functions"""
 
 import unittest
diff --git a/wqflask/tests/wqflask/marker_regression/__init__.py b/wqflask/tests/unit/wqflask/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/marker_regression/__init__.py
+++ b/wqflask/tests/unit/wqflask/__init__.py
diff --git a/wqflask/tests/wqflask/show_trait/__init__.py b/wqflask/tests/unit/wqflask/api/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/show_trait/__init__.py
+++ b/wqflask/tests/unit/wqflask/api/__init__.py
diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 84898bd1..84898bd1 100644
--- a/wqflask/tests/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
diff --git a/wqflask/tests/unit/wqflask/marker_regression/__init__.py b/wqflask/tests/unit/wqflask/marker_regression/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/__init__.py
diff --git a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..8ae0f09f 100644
--- a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
diff --git a/wqflask/tests/unit/wqflask/show_trait/__init__.py b/wqflask/tests/unit/wqflask/show_trait/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/show_trait/__init__.py
diff --git a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
index 41761944..41761944 100644
--- a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py
+++ b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..9a36132d 100644
--- a/wqflask/tests/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
diff --git a/wqflask/tests/unit/wqflask/test_markdown_routes.py b/wqflask/tests/unit/wqflask/test_markdown_routes.py
new file mode 100644
index 00000000..90e0f17c
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_markdown_routes.py
@@ -0,0 +1,54 @@
+"""Test functions in markdown utils"""
+
+import unittest
+from unittest import mock
+
+from dataclasses import dataclass
+from wqflask.markdown_routes import render_markdown
+
+
+@dataclass
+class MockRequests404:
+    status_code: int = 404
+
+
+@dataclass
+class MockRequests200:
+    status_code: int = 200
+    content: str = b"""
+# Glossary
+This is some content
+
+## Sub-heading
+This is another sub-heading"""
+
+
+class TestMarkdownRoutesFunctions(unittest.TestCase):
+    """Test cases for functions in markdown_routes"""
+
+    @mock.patch('wqflask.markdown_routes.requests.get')
+    def test_render_markdown_when_fetching_locally(self, requests_mock):
+        requests_mock.return_value = MockRequests404()
+        markdown_content = render_markdown("general/glossary/glossary.md")
+        requests_mock.assert_called_with(
+            "https://raw.githubusercontent.com"
+            "/genenetwork/gn-docs/"
+            "master/general/"
+            "glossary/glossary.md")
+        self.assertRegexpMatches(markdown_content,
+                                 "Content for general/glossary/glossary.md not available.")
+
+    @mock.patch('wqflask.markdown_routes.requests.get')
+    def test_render_markdown_when_fetching_remotely(self, requests_mock):
+        requests_mock.return_value = MockRequests200()
+        markdown_content = render_markdown("general/glossary/glossary.md")
+        requests_mock.assert_called_with(
+            "https://raw.githubusercontent.com"
+            "/genenetwork/gn-docs/"
+            "master/general/"
+            "glossary/glossary.md")
+        self.assertEqual("""<h1>Glossary</h1>
+<p>This is some content</p>
+<h2>Sub-heading</h2>
+<p>This is another sub-heading</p>""",
+                         markdown_content)
diff --git a/wqflask/tests/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py
index a33fbd4f..a33fbd4f 100644
--- a/wqflask/tests/wqflask/test_pbkdf2.py
+++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py
diff --git a/wqflask/tests/wqflask/test_user_login.py b/wqflask/tests/unit/wqflask/test_user_login.py
index 61cd9ab9..61cd9ab9 100644
--- a/wqflask/tests/wqflask/test_user_login.py
+++ b/wqflask/tests/unit/wqflask/test_user_login.py
diff --git a/wqflask/tests/wqflask/test_user_session.py b/wqflask/tests/unit/wqflask/test_user_session.py
index ebb0334a..ebb0334a 100644
--- a/wqflask/tests/wqflask/test_user_session.py
+++ b/wqflask/tests/unit/wqflask/test_user_session.py
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)