test_gene_set_selection: update tests

Author: JakaKokosar

orangecontrib/bioinformatics/tests/widgets/components/test_gene_set_selection.py

@@ -1,11 +1,11 @@
 import unittest
 
-from orangewidget.tests.base import WidgetTest
-
 from AnyQt.QtCore import Qt, QPoint
 from AnyQt.QtTest import QTest, QSignalSpy
 from AnyQt.QtWidgets import QTreeWidget, QTreeWidgetItem, QTreeWidgetItemIterator
 
+from orangewidget.tests.base import WidgetTest
+
 from Orange.data import Table, Domain, StringVariable, DiscreteVariable
 from Orange.widgets.widget import Msg, OWWidget
 from Orange.widgets.settings import SettingProvider
@@ -38,25 +38,30 @@ def setUp(self):
         self.human_tax_id: str = '9606'
         self.dicty_tax_id: str = '44689'
 
-        self.default_selection = [('GO', 'biological_process')]
-        self.marker_genes = [('Marker Genes', 'Panglao'), ('Marker Genes', 'CellMarker')]
+        self.default_selection = [('KEGG', 'Pathways')]
+        self.marker_genes = [
+            ('Marker Genes', 'Panglao'),
+            ('Marker Genes', 'CellMarker'),
+        ]
         self.gene_ontologies = [
             ('GO', 'cellular_component'),
             ('GO', 'biological_process'),
             ('GO', 'molecular_function'),
         ]
 
     def __item_iterator(self):
-        iterator = QTreeWidgetItemIterator(self.component.hierarchy_tree_widget, QTreeWidgetItemIterator.All)
+        iterator = QTreeWidgetItemIterator(
+            self.component.hierarchy_tree_widget, QTreeWidgetItemIterator.All
+        )
 
         while iterator.value():
             item: QTreeWidgetItem = iterator.value()
             if not item.childCount():
                 yield item
             iterator += 1
 
-    def __initialization(self, tax_id: str) -> None:
-        self.component.initialize(tax_id)
+    def __initialization(self) -> None:
+        self.component.initialize()
 
         # test if gene sets are shown
         gene_set_items = {item.hierarchy for item in self.__item_iterator()}
@@ -72,20 +77,20 @@ def __initialization(self, tax_id: str) -> None:
         self.assertTrue(len(selection))
         self.assertEqual(selection, self.default_selection)
 
-    def test_dictyostelium(self):
-        self.__initialization(self.dicty_tax_id)
-        self.assertEqual(self.component.gene_sets.common_org(), self.dicty_tax_id)
-
-    def test_mus_musculus(self):
-        self.__initialization(self.mouse_tax_id)
-        self.assertEqual(self.component.gene_sets.common_org(), self.mouse_tax_id)
+    # def test_dictyostelium(self):
+    #     self.__initialization()
+    #     self.assertEqual(self.component.gene_sets.common_org(), self.dicty_tax_id)
 
-    def test_homo_sapiens(self):
-        self.__initialization(self.human_tax_id)
-        self.assertEqual(self.component.gene_sets.common_org(), self.human_tax_id)
+    # def test_mus_musculus(self):
+    #     self.__initialization()
+    #     self.assertEqual(self.component.gene_sets.common_org(), self.mouse_tax_id)
+    #
+    # def test_homo_sapiens(self):
+    #     self.__initialization()
+    #     self.assertEqual(self.component.gene_sets.common_org(), self.human_tax_id)
 
     def test_selection(self):
-        self.__initialization(self.human_tax_id)
+        self.__initialization()
 
         panglao, _ = self.marker_genes
 
@@ -102,42 +107,57 @@ def test_selection(self):
         # simulate click on item but not in checkbox area.
         # checkbox status is not changed and signal is not emitted
         click_item_text = QPoint(rect.x() + 100, rect.y() + 5)
-        QTest.mouseClick(tree_widget.viewport(), Qt.LeftButton, Qt.NoModifier, click_item_text)
+        QTest.mouseClick(
+            tree_widget.viewport(), Qt.LeftButton, Qt.NoModifier, click_item_text
+        )
         self.assertFalse(len(emitted_signals))
         self.assertEqual(self.component._get_selection(), self.default_selection)
 
         # simulate click on items checkbox.
         # checkbox status is changed and signal is emitted
         click_checkbox = QPoint(rect.x() + 10, rect.y() + 5)
-        QTest.mouseClick(tree_widget.viewport(), Qt.LeftButton, Qt.NoModifier, click_checkbox)
+        QTest.mouseClick(
+            tree_widget.viewport(), Qt.LeftButton, Qt.NoModifier, click_checkbox
+        )
         self.assertTrue(len(emitted_signals))
         self.assertNotEqual(self.component._get_selection(), self.default_selection)
-        self.assertEqual(set(self.component._get_selection()), set(self.default_selection + [new_selection.hierarchy]))
+        self.assertEqual(
+            set(self.component._get_selection()),
+            set(self.default_selection + [new_selection.hierarchy]),
+        )
 
     def test_custom_gene_sets(self):
         domain = Domain(
-            [], metas=[StringVariable('genes')], class_vars=DiscreteVariable('cell_type', values=['foo', 'bar'])
+            [],
+            metas=[StringVariable('genes')],
+            class_vars=DiscreteVariable('cell_type', values=['foo', 'bar']),
         )
         data = Table.from_list(domain, [[0, 'gene1'], [1, 'gene2'], [1, 'gene3']])
         data.name = 'custom_gene_sets'
         data.attributes[TableAnnotation.tax_id] = self.human_tax_id
         data.attributes[TableAnnotation.gene_as_attr_name] = False
         data.attributes[TableAnnotation.gene_id_column] = 'genes'
 
-        self.__initialization(self.human_tax_id)
+        self.__initialization()
         self.component.initialize_custom_gene_sets(data)
 
         self.assertTrue(self.component.gene_sets_combobox.isEnabled())
         self.assertEqual(self.component.custom_gene_set_hierarchy, (data.name,))
         self.assertEqual(self.component._get_selection(), [(data.name,)])
-        self.assertIn((data.name,), self.component.gene_sets.map_hierarchy_to_sets().keys())
+        self.assertIn(
+            (data.name,), self.component.gene_sets.map_hierarchy_to_sets().keys()
+        )
 
         emitted_signals: QSignalSpy = QSignalSpy(self.component.selection_changed)
         simulate.combobox_run_through_all(self.component.gene_sets_combobox)
-        self.assertEqual(len(emitted_signals), len(data.domain.metas) + len(data.domain.class_vars))
+        self.assertEqual(
+            len(emitted_signals), len(data.domain.metas) + len(data.domain.class_vars)
+        )
 
         self.component.initialize_custom_gene_sets(None)
-        self.assertNotIn((data.name,), self.component.gene_sets.map_hierarchy_to_sets().keys())
+        self.assertNotIn(
+            (data.name,), self.component.gene_sets.map_hierarchy_to_sets().keys()
+        )
         self.assertIsNone(self.component.custom_gene_set_hierarchy)
         self.assertTrue(self.component.custom_gs_box.isHidden())