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use unittest assert methods instead of assert

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Charlotte Weaver
2018-07-17 11:01:38 -07:00
parent a5423a6911
commit fdaaaf69a2
1 changed files with 20 additions and 20 deletions
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40
server/test/test_scanpy_engine.py
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@@ -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()
unittest.main()