Merge pull request #145 from Knowledge-Graph-Hub/add_tests

Add tests
Knowledge-Graph-Hub · May 9, 2020 · 985eab2 · 985eab2
2 parents 83e5f46 + ae58c67
commit 985eab2
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Showing 4 changed files with 44 additions and 1 deletion.
diff --git a/tests/resources/gene2ensembl.gz b/tests/resources/gene2ensembl.gz
diff --git a/tests/resources/gene_info.gz b/tests/resources/gene_info.gz
diff --git a/tests/test_run.py b/tests/test_run.py
@@ -24,9 +24,11 @@ def test_transform(self):
 
     def test_merge_missing_file_error(self):
         with self.assertRaises(FileNotFoundError) as context:
-           self.runner.invoke(catch_exceptions=False,
+            result = self.runner.invoke(catch_exceptions=False,
                                         cli=load,
                                         args=['-y',
                                               'tests/resources/merge_MISSING_FILE.yaml']
                                         )
+            self.assertNotEqual(result.exit_code, 0)
+            self.assertRegexpMatches(result.output, "does not exist")
 
diff --git a/tests/test_transform_class.py b/tests/test_transform_class.py
@@ -2,7 +2,19 @@
 from unittest import TestCase
 
 from parameterized import parameterized
+from kg_covid_19.transform import DATA_SOURCES
 from kg_covid_19.transform_utils.transform import Transform
+from kg_covid_19.transform_utils.drug_central.drug_central import DrugCentralTransform
+from kg_covid_19.transform_utils.intact.intact import IntAct
+from kg_covid_19.transform_utils.ontology import OntologyTransform
+from kg_covid_19.transform_utils.ontology.ontology_transform import ONTOLOGIES
+from kg_covid_19.transform_utils.\
+    sars_cov_2_gene_annot.sars_cov_2_gene_annot import SARSCoV2GeneAnnot
+from kg_covid_19.transform_utils.pharmgkb import PharmGKB
+from kg_covid_19.transform_utils.scibite_cord import ScibiteCordTransform
+from kg_covid_19.transform_utils.string_ppi import StringTransform
+from kg_covid_19.transform_utils.ttd.ttd import TTDTransform
+from kg_covid_19.transform_utils.zhou_host_proteins.zhou_transform import ZhouTransform
 
 
 class TestTransform(TestCase):
@@ -30,6 +42,35 @@ def test_attributes(self, attr, default):
         self.assertTrue(hasattr(self.transform_instance, attr))
         self.assertEqual(getattr(self.transform_instance, attr), default)
 
+    @parameterized.expand([
+        ('DEFAULT_INPUT_DIR', 'data/raw'),
+        ('DEFAULT_OUTPUT_DIR', 'data/transformed')])
+    def test_default_dir(self, dir_var_name, dir_var_value):
+        self.assertEqual(getattr(Transform, dir_var_name), dir_var_value)
+
+    @parameterized.expand(list(DATA_SOURCES.keys()),)
+    def test_transform_child_classes(self, src_name):
+        """
+        Make sure Transform child classes:
+        - properly set default input_dir and output_dir
+        - properly pass and set input_dir and output from constructor
+        - implement run()
+
+        :param src_name:
+        :return: None
+        """
+        input_dir = os.path.join('tests','resources')
+        output_dir = os.path.join('output')
+        def_input_dir = os.path.join('data', 'raw')
+        def_output_dir = os.path.join('data', 'transformed')
+
+        t = DATA_SOURCES[src_name](input_dir=input_dir, output_dir=output_dir)
+        self.assertEqual(t.input_base_dir, input_dir)
+        self.assertEqual(t.output_base_dir, output_dir)
+        self.assertTrue(hasattr(t, 'run'))
+        self.assertEqual(t.DEFAULT_INPUT_DIR, def_input_dir)
+        self.assertEqual(t.DEFAULT_OUTPUT_DIR, def_output_dir)
+
 
 class TransformChildClass(Transform):
     def __init__(self):