From fdaaaf69a241e724db54815402bb1c5c956035c7 Mon Sep 17 00:00:00 2001 From: Charlotte Weaver Date: Tue, 17 Jul 2018 11:01:38 -0700 Subject: [PATCH] use unittest assert methods instead of assert --- server/test/test_scanpy_engine.py | 40 +++++++++++++++---------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/server/test/test_scanpy_engine.py b/server/test/test_scanpy_engine.py index 1e7d91d5..e99198ca 100644 --- a/server/test/test_scanpy_engine.py +++ b/server/test/test_scanpy_engine.py @@ -8,61 +8,61 @@ class UtilTest(unittest.TestCase): self.data = ScanpyEngine("example-dataset/", schema="data_schema.json") def test_init(self): - assert self.data.cell_count == 2638 - assert self.data.gene_count == 1838 + self.assertEqual(self.data.cell_count, 2638) + self.assertEqual(self.data.gene_count, 1838) epsilon = 0.000005 - assert self.data.data.X[0,0] - -0.17146951 < epsilon + self.assertTrue(self.data.data.X[0,0] - -0.17146951 < epsilon) def test_schema(self): - assert self.data.schema == {'CellName': {'type': 'string', 'variabletype': 'categorical', 'displayname': 'Name', 'include': True}, 'n_genes': {'type': 'int', 'variabletype': 'continuous', 'displayname': 'Num Genes', 'include': True}, 'percent_mito': {'type': 'float', 'variabletype': 'continuous', 'displayname': 'Mitochondrial Percentage', 'include': True}, 'n_counts': {'type': 'float', 'variabletype': 'continuous', 'displayname': 'Num Counts', 'include': True}, 'louvain': {'type': 'string', 'variabletype': 'categorical', 'displayname': 'Louvain Cluster', 'include': True}} + self.assertEqual(self.data.schema, {'CellName': {'type': 'string', 'variabletype': 'categorical', 'displayname': 'Name', 'include': True}, 'n_genes': {'type': 'int', 'variabletype': 'continuous', 'displayname': 'Num Genes', 'include': True}, 'percent_mito': {'type': 'float', 'variabletype': 'continuous', 'displayname': 'Mitochondrial Percentage', 'include': True}, 'n_counts': {'type': 'float', 'variabletype': 'continuous', 'displayname': 'Num Counts', 'include': True}, 'louvain': {'type': 'string', 'variabletype': 'categorical', 'displayname': 'Louvain Cluster', 'include': True}}) def test_cells(self): cells = self.data.cells() - assert "AAACATACAACCAC-1" in cells - assert len(cells) == 2638 + self.assertIn("AAACATACAACCAC-1", cells) + self.assertEqual(len(cells), 2638) def test_genes(self): genes = self.data.genes() - assert "SEPT4" in genes - assert len(genes) == 1838 + self.assertIn("SEPT4", genes) + self.assertEqual(len(genes), 1838) def test_filter_categorical(self): filter = {"louvain": {"variable_type": "categorical", "value_type": "string", "query": ["B cells"]}} filtered_data = self.data.filter_cells(filter) - assert filtered_data.shape == (342, 1838) + self.assertEqual(filtered_data.shape, (342, 1838)) louvain_vals = filtered_data.obs['louvain'].tolist() - assert "B cells" in louvain_vals - assert "NK cells" not in louvain_vals + self.assertIn("B cells", louvain_vals) + self.assertNotIn("NK cells", louvain_vals) def test_filter_continuous(self): # print(self.data.data.obs["n_genes"].tolist()) filter = {"n_genes": {"variable_type": "continuous", "value_type": "int", "query": {"min": 300, "max": 400}}} filtered_data = self.data.filter_cells(filter) - assert filtered_data.shape == (71, 1838) + self.assertEqual(filtered_data.shape, (71, 1838)) n_genes_vals = filtered_data.obs['n_genes'].tolist() for val in n_genes_vals: - assert 300 <= val <= 400 + self.assertTrue(300 <= val <= 400) def test_metadata(self): metadata = self.data.metadata(df=self.data.data) - assert len(metadata) == 2638 - assert 'louvain' in metadata[0] + self.assertEqual(len(metadata), 2638) + self.assertIn('louvain', metadata[0]) def test_create_graph(self): graph = self.data.create_graph(df=self.data.data) - assert graph[0][1] == 0.5545382653143183 - assert graph[0][2] == 0.6021833809031731 + self.assertEqual(graph[0][1], 0.5545382653143183) + self.assertEqual(graph[0][2], 0.6021833809031731) def test_diffexp(self): diffexp = self.data.diffexp(["AAACATACAACCAC-1", "AACCGATGGTCATG-1"], ["CCGATAGACCTAAG-1", "GGTGGAGAAGTAGA-1"], 0.5, 7) - assert diffexp["celllist1"]["topgenes"] == ['EBNA1BP2', 'DIAPH1', 'SLC25A11', 'SNRNP27', 'COMMD8', 'COTL1', 'GTF3A'] + self.assertEqual(diffexp["celllist1"]["topgenes"], ['EBNA1BP2', 'DIAPH1', 'SLC25A11', 'SNRNP27', 'COMMD8', 'COTL1', 'GTF3A']) def test_expression(self): expression = self.data.expression(cells=["AAACATACAACCAC-1"]) data_exp = self.data.data[["AAACATACAACCAC-1"], :].X for idx in range(len(expression["cells"][0]["e"])): - assert expression["cells"][0]["e"][idx] == data_exp[idx] + self.assertEqual(expression["cells"][0]["e"][idx], data_exp[idx]) if __name__ == '__main__': - unittest.main() \ No newline at end of file + unittest.main()