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Code Issues Packages Projects Releases Wiki Activity

Move jsonification to engine level (#511)

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This commit is contained in:
Charlotte Weaver
2018-12-18 21:14:24 -08:00
committed by GitHub
parent 6af7708d62
commit f0f7200f0b
10 changed files with 657 additions and 133 deletions
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server/test/test_scanpy_engine.py
+71 -32
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@@ -44,22 +44,39 @@ class UtilTest(unittest.TestCase):
self.data._validate_data_types()
def test_filter_idx(self):
filter_ = {"filter": {"var": {"index": [1, 99, [200, 300]]}, "obs": {"index": [1, 99, [1000, 2000]]}}}
filter_ = {
"filter": {
"var": {"index": [1, 99, [200, 300]]},
"obs": {"index": [1, 99, [1000, 2000]]},
}
}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape, (1002, 102))
def test_filter_annotation(self):
filter_ = {
"filter": {"obs": {"annotation_value": [{"name": "louvain", "values": ["NK cells", "CD8 T cells"]}]}}
"filter": {
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]}
]
}
}
}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape, (470, 1838))
filter_ = {"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}}
filter_ = {
"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}
}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape, (497, 1838))
def test_filter_annotation_no_uns(self):
filter_ = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
filter_ = {
"filter": {
"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}
}
}
data = self.data.filter_dataframe(filter_["filter"])
self.assertEqual(data.shape[1], 1)
@@ -90,36 +107,45 @@ class UtilTest(unittest.TestCase):
def test_schema_produces_error(self):
self.data.data.obs["time"] = Series(
list([time.time() for i in range(self.data.cell_count)]), dtype="datetime64[ns]"
list([time.time() for i in range(self.data.cell_count)]),
dtype="datetime64[ns]",
)
with pytest.raises(TypeError):
self.data._create_schema()
def test_config(self):
self.assertEqual(self.data.features["layout"]["obs"], {"available": True, "interactiveLimit": 50000})
self.assertEqual(
self.data.features["layout"]["obs"],
{"available": True, "interactiveLimit": 50000},
)
def test_layout(self):
layout = self.data.layout(None)
self.assertEqual(layout["ndims"], 2)
self.assertEqual(len(layout["coordinates"]), 2638)
self.assertEqual(layout["coordinates"][0][0], 0)
for idx, val in enumerate(layout["coordinates"]):
layout = json.loads(self.data.layout(None))
self.assertEqual(layout["layout"]["ndims"], 2)
self.assertEqual(len(layout["layout"]["coordinates"]), 2638)
self.assertEqual(layout["layout"]["coordinates"][0][0], 0)
for idx, val in enumerate(layout["layout"]["coordinates"]):
self.assertLessEqual(val[1], 1)
self.assertLessEqual(val[2], 1)
def test_annotations(self):
annotations = self.data.annotation(None, "obs")
self.assertEqual(annotations["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
annotations = json.loads(self.data.annotation(None, "obs"))
self.assertEqual(
annotations["names"],
["name", "n_genes", "percent_mito", "n_counts", "louvain"],
)
self.assertEqual(len(annotations["data"]), 2638)
annotations = self.data.annotation(None, "var")
annotations = json.loads(self.data.annotation(None, "var"))
self.assertEqual(annotations["names"], ["name", "n_cells"])
self.assertEqual(len(annotations["data"]), 1838)
def test_annotation_fields(self):
annotations = self.data.annotation(None, "obs", ["n_genes", "n_counts"])
annotations = json.loads(
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(None, "var", ["name"])
annotations = json.loads(self.data.annotation(None, "var", ["name"]))
self.assertEqual(annotations["names"], ["name"])
self.assertEqual(len(annotations["data"]), 1838)
@@ -127,45 +153,54 @@ class UtilTest(unittest.TestCase):
filter_ = {
"filter": {
"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]},
"var": {"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]},
"var": {
"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]
},
}
}
annotations = self.data.annotation(filter_["filter"], "obs")
self.assertEqual(annotations["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
annotations = json.loads(self.data.annotation(filter_["filter"], "obs"))
self.assertEqual(
annotations["names"],
["name", "n_genes", "percent_mito", "n_counts", "louvain"],
)
self.assertEqual(len(annotations["data"]), 497)
annotations = self.data.annotation(filter_["filter"], "var")
annotations = json.loads(self.data.annotation(filter_["filter"], "var"))
self.assertEqual(annotations["names"], ["name", "n_cells"])
self.assertEqual(len(annotations["data"]), 2)
def test_filtered_layout(self):
filter_ = {"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}}
layout = self.data.layout(filter_["filter"])
self.assertEqual(len(layout["coordinates"]), 497)
filter_ = {
"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}
}
layout = json.loads(self.data.layout(filter_["filter"]))
self.assertEqual(len(layout["layout"]["coordinates"]), 497)
def test_diffexp_topN(self):
f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
result = self.data.diffexp_topN(f1["filter"], f2["filter"])
result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
self.assertEqual(len(result), 10)
result = self.data.diffexp_topN(f1["filter"], f2["filter"], 20)
result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"], 20))
self.assertEqual(len(result), 20)
def test_data_frame(self):
data_frame_obs = self.data.data_frame(None, "obs")
data_frame_obs = json.loads(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(None, "var")
data_frame_var = json.loads(self.data.data_frame(None, "var"))
self.assertEqual(len(data_frame_var["var"]), 1838)
self.assertEqual(len(data_frame_var["obs"]), 2638)
def test_filtered_data_frame(self):
filter_ = {"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}}
data_frame_obs = self.data.data_frame(filter_["filter"], "obs")
filter_ = {
"filter": {"obs": {"annotation_value": [{"name": "n_counts", "min": 3000}]}}
}
data_frame_obs = json.loads(self.data.data_frame(filter_["filter"], "obs"))
self.assertEqual(len(data_frame_obs["var"]), 1838)
self.assertEqual(len(data_frame_obs["obs"]), 497)
self.assertIsInstance(data_frame_obs["obs"][0], (list, tuple))
self.assertEqual(type(data_frame_obs["var"][0]), int)
data_frame_var = self.data.data_frame(filter_["filter"], "var")
data_frame_var = json.loads(self.data.data_frame(filter_["filter"], "var"))
self.assertEqual(len(data_frame_var["var"]), 1838)
self.assertEqual(len(data_frame_var["obs"]), 497)
self.assertIsInstance(data_frame_var["var"][0], (list, tuple))
@@ -173,8 +208,12 @@ class UtilTest(unittest.TestCase):
def test_data_single_gene(self):
for axis in ["obs", "var"]:
filter_ = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
data_frame_var = self.data.data_frame(filter_["filter"], axis)
filter_ = {
"filter": {
"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}
}
}
data_frame_var = json.loads(self.data.data_frame(filter_["filter"], axis))
if axis == "obs":
self.assertEqual(type(data_frame_var["var"][0]), int)
self.assertIsInstance(data_frame_var["obs"][0], (list, tuple))