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Code Issues Packages Projects Releases Wiki Activity

Filter in engine (#307)

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* Add empty filter case

* Filtering dataframes moved to engine instead of rest

* minor changes from PR review

* Minor fixes from PR review

Pass {} instead of none if no filter
chain exceptions
typos
This commit is contained in:
Charlotte Weaver
2018-10-11 15:23:31 -07:00
committed by GitHub
parent ee0b066eb6
commit 210787cb5d
5 changed files with 127 additions and 93 deletions
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server/test/test_scanpy_engine.py
+15 -21
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@@ -120,7 +120,7 @@ class UtilTest(unittest.TestCase):
self.assertEqual(self.data.features["layout"]["obs"], {'available': True, 'interactiveLimit': 15000})
def test_layout(self):
layout = self.data.layout(self.data.data)
layout = self.data.layout(None)
self.assertEqual(layout["ndims"], 2)
self.assertEqual(len(layout["coordinates"]), 2638)
self.assertEqual(layout["coordinates"][0][0], 0)
@@ -129,18 +129,18 @@ class UtilTest(unittest.TestCase):
self.assertLessEqual(val[2], 1)
def test_annotations(self):
annotations = self.data.annotation(self.data.data, "obs")
annotations = self.data.annotation(None, "obs")
self.assertEqual(annotations["names"], ["n_genes", "percent_mito", "n_counts", "louvain", "name"])
self.assertEqual(len(annotations["data"]), 2638)
annotations = self.data.annotation(self.data.data, "var")
annotations = self.data.annotation(None, "var")
self.assertEqual(annotations["names"], ["n_cells", "name"])
self.assertEqual(len(annotations["data"]), 1838)
def test_annotation_fields(self):
annotations = self.data.annotation(self.data.data, "obs", ["n_genes", "n_counts"])
annotations = self.data.annotation(None, "obs", ["n_genes", "n_counts"])
self.assertEqual(annotations["names"], ["n_genes", "n_counts"])
self.assertEqual(len(annotations["data"]), 2638)
annotations = self.data.annotation(self.data.data, "var", ["name"])
annotations = self.data.annotation(None, "var", ["name"])
self.assertEqual(annotations["names"], ["name"])
self.assertEqual(len(annotations["data"]), 1838)
@@ -159,11 +159,10 @@ class UtilTest(unittest.TestCase):
}
}
}
data = self.data.filter_dataframe(filter_["filter"])
annotations = self.data.annotation(data, "obs")
annotations = self.data.annotation(filter_["filter"], "obs")
self.assertEqual(annotations["names"], ["n_genes", "percent_mito", "n_counts", "louvain", "name"])
self.assertEqual(len(annotations["data"]), 497)
annotations = self.data.annotation(data, "var")
annotations = self.data.annotation(filter_["filter"], "var")
self.assertEqual(annotations["names"], ["n_cells", "name"])
self.assertEqual(len(annotations["data"]), 2)
@@ -177,8 +176,7 @@ class UtilTest(unittest.TestCase):
}
}
}
data = self.data.filter_dataframe(filter_["filter"])
layout = self.data.layout(data)
layout = self.data.layout(filter_["filter"])
self.assertEqual(len(layout["coordinates"]), 497)
def test_diffexp(self):
@@ -189,7 +187,6 @@ class UtilTest(unittest.TestCase):
}
}
}
df1 = self.data.filter_dataframe(f1["filter"])
f2 = {
"filter": {
"obs": {
@@ -197,19 +194,18 @@ class UtilTest(unittest.TestCase):
}
}
}
df2 = self.data.filter_dataframe(f2["filter"])
result = self.data.diffexp(df1, df2)
result = self.data.diffexp(f1["filter"], f2["filter"])
self.assertEqual(len(result), 10)
var_idx = [i[0] for i in result]
self.assertEqual(var_idx, sorted(var_idx))
result = self.data.diffexp(df1, df2, 20)
result = self.data.diffexp(f1["filter"], f2["filter"], 20)
self.assertEqual(len(result), 20)
def test_data_frame(self):
data_frame_obs = self.data.data_frame(self.data.data, "obs")
data_frame_obs = self.data.data_frame(None, "obs")
self.assertEqual(len(data_frame_obs["var"]), 1838)
self.assertEqual(len(data_frame_obs["obs"]), 2638)
data_frame_var = self.data.data_frame(self.data.data, "var")
data_frame_var = self.data.data_frame(None, "var")
self.assertEqual(len(data_frame_var["var"]), 1838)
self.assertEqual(len(data_frame_var["obs"]), 2638)
@@ -223,13 +219,12 @@ class UtilTest(unittest.TestCase):
}
}
}
data = self.data.filter_dataframe(filter_["filter"])
data_frame_obs = self.data.data_frame(data, "obs")
data_frame_obs = self.data.data_frame(filter_["filter"], "obs")
self.assertEqual(len(data_frame_obs["var"]), 1838)
self.assertEqual(len(data_frame_obs["obs"]), 497)
self.assertEqual(type(data_frame_obs["obs"][0]), list)
self.assertEqual(type(data_frame_obs["var"][0]), int)
data_frame_var = self.data.data_frame(data, "var")
data_frame_var = self.data.data_frame(filter_["filter"], "var")
self.assertEqual(len(data_frame_var["var"]), 1838)
self.assertEqual(len(data_frame_var["obs"]), 497)
self.assertEqual(type(data_frame_var["var"][0]), list)
@@ -246,8 +241,7 @@ class UtilTest(unittest.TestCase):
}
}
}
data = self.data.filter_dataframe(filter_["filter"], include_uns=False)
data_frame_var = self.data.data_frame(data, axis)
data_frame_var = self.data.data_frame(filter_["filter"], axis)
if axis == "obs":
self.assertEqual(type(data_frame_var["var"][0]), int)
self.assertEqual(type(data_frame_var["obs"][0]), list)