diff --git a/MANIFEST.in b/MANIFEST.in index ec6f0e6c..b881e298 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,3 @@ recursive-include server/app/web/templates * recursive-include server/app/web/static * + diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py index 142f87a7..4e580efc 100644 --- a/server/app/scanpy_engine/scanpy_engine.py +++ b/server/app/scanpy_engine/scanpy_engine.py @@ -61,11 +61,11 @@ class ScanpyEngine(CXGDriver): else: min_ = value["query"]["min"] max_ = value["query"]["max"] - if min_: + if min_ is not None: key_idx = np.array((getattr(self.data.obs, key) >= min_).data) cell_idx = np.logical_and(cell_idx, key_idx) - if max_: - key_idx = np.array((getattr(self.data.obs, key) <= min_).data) + if max_ is not None: + key_idx = np.array((getattr(self.data.obs, key) <= max_).data) cell_idx = np.logical_and(cell_idx, key_idx) return self.data[cell_idx, :] @@ -124,6 +124,7 @@ class ScanpyEngine(CXGDriver): expression_1 = self.data.X[cells_idx_1, :] expression_2 = self.data.X[cells_idx_2, :] diff_exp = stats.ttest_ind(expression_1, expression_2) + # TODO break this up into functions set1 = np.logical_and(diff_exp.pvalue < pval, diff_exp.statistic > 0) set2 = np.logical_and(diff_exp.pvalue < pval, diff_exp.statistic < 0) stat1 = diff_exp.statistic[set1] diff --git a/server/requirements.txt b/server/requirements.txt index 21b90d84..7ab96abb 100644 --- a/server/requirements.txt +++ b/server/requirements.txt @@ -1,5 +1,5 @@ aniso8601==3.0.2 -anndata==0.6.4 +anndata==0.6.1 certifi==2018.4.16 chardet==3.0.4 click==6.7 diff --git a/server/test/test_filter.py b/server/test/test_filter.py index f46cd14a..3641fee1 100644 --- a/server/test/test_filter.py +++ b/server/test/test_filter.py @@ -1,9 +1,7 @@ import unittest - from unittest.mock import MagicMock -import sys -sys.path.insert(0, "../app") -from util.filter import _convert_variable, parse_filter + +from server.app.util.filter import _convert_variable, parse_filter class UtilTest(unittest.TestCase): @@ -72,3 +70,6 @@ class UtilTest(unittest.TestCase): filterMock.getlist.return_value = ["0,*"] query = parse_filter(filterMock, self.schema) assert query == {"n_genes": {"variable_type": "continuous", "value_type": "int", "query": {"min": 0, "max": None}}} + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/server/test/test_scanpy_engine.py b/server/test/test_scanpy_engine.py new file mode 100644 index 00000000..e99198ca --- /dev/null +++ b/server/test/test_scanpy_engine.py @@ -0,0 +1,68 @@ +import unittest + +from server.app.scanpy_engine.scanpy_engine import ScanpyEngine + + +class UtilTest(unittest.TestCase): + def setUp(self): + self.data = ScanpyEngine("example-dataset/", schema="data_schema.json") + + def test_init(self): + self.assertEqual(self.data.cell_count, 2638) + self.assertEqual(self.data.gene_count, 1838) + epsilon = 0.000005 + self.assertTrue(self.data.data.X[0,0] - -0.17146951 < epsilon) + + def test_schema(self): + 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() + self.assertIn("AAACATACAACCAC-1", cells) + self.assertEqual(len(cells), 2638) + + def test_genes(self): + genes = self.data.genes() + 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) + self.assertEqual(filtered_data.shape, (342, 1838)) + louvain_vals = filtered_data.obs['louvain'].tolist() + 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) + self.assertEqual(filtered_data.shape, (71, 1838)) + n_genes_vals = filtered_data.obs['n_genes'].tolist() + for val in n_genes_vals: + self.assertTrue(300 <= val <= 400) + + def test_metadata(self): + metadata = self.data.metadata(df=self.data.data) + self.assertEqual(len(metadata), 2638) + self.assertIn('louvain', metadata[0]) + + def test_create_graph(self): + graph = self.data.create_graph(df=self.data.data) + 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) + 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"])): + self.assertEqual(expression["cells"][0]["e"][idx], data_exp[idx]) + + +if __name__ == '__main__': + unittest.main()