From 30f305c1b87b4b6c4f308b15d5ae9248dc367e14 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 22 Sep 2022 06:33:47 +0300
Subject: Provide database cursor as argument for TheSpecies and Chromosomes

Provide the database cursor as an argument to the methods of the two
classes:

* wqflask.base.species.TheSpecies
* wqflask.base.species.Chromosomes

Also update dependent code to initialise and pass the cursor where
these classes are used.
---
 wqflask/tests/unit/base/test_species.py | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

(limited to 'wqflask/tests/unit/base')

diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py
index d7ba30a3..f12bde6d 100644
--- a/wqflask/tests/unit/base/test_species.py
+++ b/wqflask/tests/unit/base/test_species.py
@@ -30,17 +30,14 @@ class MockDataset:
      (None, "Random Dataset", None, 1)))
 def test_species(mocker, species_name, dataset,
                  expected_name, chromosome_param):
-    mock_conn = mocker.patch("base.species.database_connection")
-    mock_conn.return_value.__enter__.return_value = mocker.MagicMock()
     _c = mocker.patch("base.species.Chromosomes",
                       return_value=chromosome_param)
-    with mock_conn() as conn:
-        test_species = TheSpecies(dataset=dataset,
-                                  species_name=species_name)
-        _c.assert_called_with(conn=conn, species=species_name,
-                              dataset=dataset)
-        assert test_species.name == expected_name
-        assert test_species.chromosomes == chromosome_param
+    test_species = TheSpecies(dataset=dataset,
+                              species_name=species_name)
+    _c.assert_called_with(species=species_name,
+                          dataset=dataset)
+    assert test_species.name == expected_name
+    assert test_species.chromosomes == chromosome_param
 
 
 @pytest.mark.parametrize(
@@ -74,9 +71,8 @@ def test_create_chromosomes(mocker, species, dataset, expected_call):
         cursor.fetchall.return_value = (("1", 2, 10,),
                                         ("2", 3, 11,),
                                         ("4", 5, 15,),)
-        _c = Chromosomes(conn=mock_conn,
-                         dataset=dataset, species=species)
-        assert _c.chromosomes == OrderedDict([
+        _c = Chromosomes(dataset=dataset, species=species)
+        assert _c.chromosomes(cursor) == OrderedDict([
             ("1", IndChromosome("1", 10)),
             ("2", IndChromosome("2", 11)),
             ("4", IndChromosome("4", 15)),
-- 
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