mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-27 21:08:11 +08:00
Flatbuffer cleanup (#598)
* dead code and route removal * more dead code cleanup * fix scanpy_engine tests * lint * add missing catch in filter parsing * update scanpy NaN tests * more fbs tests and dead test removal * remove forced default for content type negotiation * bit of cleanup * more fbs test cleanup * lint * remove swagger * swagger cleanup * lint * correctly handle lack of templates * more dead code removal * remove unused files * fix dev build * lint
This commit is contained in:
Bruce Martin
+71
-292
@@ -57,16 +57,6 @@ class EndPoints(unittest.TestCase):
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self.assertEqual(result_data["config"]["displayNames"]["dataset"], "pbmc3k")
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self.assertEqual(len(result_data["config"]["features"]), 4)
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def test_get_layout(self):
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endpoint = "layout/obs"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["layout"]["ndims"], 2)
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self.assertEqual(len(result_data["layout"]["coordinates"]), 2638)
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def test_get_layout_fbs(self):
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endpoint = "layout/obs"
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url = f"{URL_BASE}{endpoint}"
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@@ -82,53 +72,11 @@ class EndPoints(unittest.TestCase):
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self.assertIsNone(df['row_idx'])
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self.assertEqual(len(df['columns']), df['n_cols'])
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# def test_put_layout(self):
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# endpoint = "layout/obs"
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# url = f"{URL_BASE}{endpoint}"
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# obs_filter = {
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# "filter": {
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# "obs": {
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# "annotation_value": [
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# {"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
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# {"name": "n_counts", "min": 3000},
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# ],
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# "index": [1, 99, [1000, 2000]]
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# }
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# }
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# }
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# result = self.session.put(url, json=obs_filter)
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# self.assertEqual(result.status_code, HTTPStatus.OK)
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# result_data = result.json()
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# self.assertEqual(len(result_data["layout"]["coordinates"]), 15)
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def test_bad_filter(self):
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endpoints = ["annotations/obs", "annotations/var", "data/obs", "data/var"]
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for endpoint in endpoints:
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url = f"{URL_BASE}{endpoint}"
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result = self.session.put(url, json=BAD_FILTER)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_get_annotations_obs(self):
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endpoint = "annotations/obs"
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endpoint = "data/var"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
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self.assertEqual(len(result_data["data"]), 2638)
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self.assertEqual(len(result_data["data"][0]), 6)
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def test_get_annotations_obs_keys(self):
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endpoint = "annotations/obs"
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query = "annotation-name=n_genes&annotation-name=percent_mito"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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self.assertEqual(result.status_code, HTTPStatus.OK)
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result_data = result.json()
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self.assertEqual(result_data["names"], ["n_genes", "percent_mito"])
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self.assertEqual(len(result_data["data"][0]), 3)
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result = self.session.put(url, json=BAD_FILTER)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_get_annotations_obs_fbs(self):
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endpoint = "annotations/obs"
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@@ -146,6 +94,23 @@ class EndPoints(unittest.TestCase):
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self.assertEqual(len(df['columns']), df['n_cols'])
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self.assertListEqual(df['col_idx'], ['name', 'n_genes', 'percent_mito', 'n_counts', 'louvain'])
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def test_get_annotations_obs_keys_fbs(self):
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endpoint = "annotations/obs"
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query = "annotation-name=n_genes&annotation-name=percent_mito"
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url = f"{URL_BASE}{endpoint}?{query}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df['n_rows'], 2638)
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self.assertEqual(df['n_cols'], 2)
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self.assertIsNotNone(df['columns'])
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self.assertIsNotNone(df['col_idx'])
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self.assertIsNone(df['row_idx'])
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self.assertEqual(len(df['columns']), df['n_cols'])
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self.assertListEqual(df['col_idx'], ['n_genes', 'percent_mito'])
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def test_get_annotations_obs_error(self):
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endpoint = "annotations/obs"
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query = "annotation-name=notakey"
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@@ -153,50 +118,6 @@ class EndPoints(unittest.TestCase):
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_put_annotations_obs(self):
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endpoint = "annotations/obs"
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url = f"{URL_BASE}{endpoint}"
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obs_filter = {
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"filter": {
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"obs": {
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"annotation_value": [
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{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
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{"name": "n_counts", "min": 3000},
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],
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"index": [1, 99, [1000, 2000]],
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}
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}
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}
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result = self.session.put(url, json=obs_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
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self.assertEqual(len(result_data["data"]), 15)
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def test_filter_put_annotations_obs(self):
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endpoint = "annotations/obs"
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query = "annotation-name=n_genes&annotation-name=percent_mito"
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url = f"{URL_BASE}{endpoint}?{query}"
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obs_filter = {
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"filter": {
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"obs": {
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"annotation_value": [
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{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
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{"name": "n_counts", "min": 3000},
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],
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"index": [1, 99, [1000, 2000]],
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}
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}
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}
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result = self.session.put(url, json=obs_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["n_genes", "percent_mito"])
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self.assertEqual(len(result_data["data"][0]), 3)
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self.assertEqual(len(result_data["data"]), 15)
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def test_diff_exp(self):
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endpoint = "diffexp/obs"
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url = f"{URL_BASE}{endpoint}"
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@@ -227,28 +148,6 @@ class EndPoints(unittest.TestCase):
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result_data = result.json()
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self.assertEqual(len(result_data), 10)
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def test_get_annotations_var(self):
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endpoint = "annotations/var"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["name", "n_cells"])
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self.assertEqual(len(result_data["data"]), 1838)
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self.assertEqual(len(result_data["data"][0]), 3)
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def test_get_annotations_var_keys(self):
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endpoint = "annotations/var"
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query = "annotation-name=n_cells"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["n_cells"])
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self.assertEqual(len(result_data["data"][0]), 2)
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def test_get_annotations_var_fbs(self):
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endpoint = "annotations/var"
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url = f"{URL_BASE}{endpoint}"
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@@ -265,6 +164,23 @@ class EndPoints(unittest.TestCase):
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self.assertEqual(len(df['columns']), df['n_cols'])
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self.assertListEqual(df['col_idx'], ['name', 'n_cells'])
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def test_get_annotations_var_keys_fbs(self):
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endpoint = "annotations/var"
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query = "annotation-name=n_cells"
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url = f"{URL_BASE}{endpoint}?{query}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df['n_rows'], 1838)
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self.assertEqual(df['n_cols'], 1)
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self.assertIsNotNone(df['columns'])
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self.assertIsNotNone(df['col_idx'])
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self.assertIsNone(df['row_idx'])
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self.assertEqual(len(df['columns']), df['n_cols'])
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self.assertListEqual(df['col_idx'], ['n_cells'])
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def test_get_annotations_var_error(self):
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endpoint = "annotations/var"
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query = "annotation-name=notakey"
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@@ -272,95 +188,36 @@ class EndPoints(unittest.TestCase):
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
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def test_put_annotations_var(self):
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endpoint = "annotations/var"
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url = f"{URL_BASE}{endpoint}"
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var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]}}}
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result = self.session.put(url, json=var_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["name", "n_cells"])
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self.assertEqual(len(result_data["data"]), 2)
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def test_filter_put_annotations_var(self):
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endpoint = "annotations/var"
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query = "annotation-name=n_cells"
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url = f"{URL_BASE}{endpoint}?{query}"
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var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["ATAD3C", "RER1"]}]}}}
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result = self.session.put(url, json=var_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(result_data["names"], ["n_cells"])
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self.assertEqual(len(result_data["data"][0]), 2)
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self.assertEqual(len(result_data["data"]), 2)
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def test_get_data(self):
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for axis in ["obs", "var"]:
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endpoint = f"data/{axis}"
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query = "accept-type=application/json"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(len(result_data["obs"]), 2638)
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def test_data_mimetype_error(self):
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for axis in ["obs", "var"]:
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endpoint = f"data/{axis}"
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query = "accept-type=xxx"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "sdkljfa;dsjalkj"}
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result = self.session.get(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
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endpoint = f"data/var"
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header = {"Accept": "xxx"}
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url = f"{URL_BASE}{endpoint}"
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result = self.session.put(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.NOT_ACCEPTABLE)
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def test_json_default(self):
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for axis in ["obs", "var"]:
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endpoint = f"data/{axis}"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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def test_data_filter(self):
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for axis in ["obs", "var"]:
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endpoint = f"data/{axis}"
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query = "accept-type=application/json&obs:louvain=NK cells&obs:louvain=CD8 T cells&obs:n_counts=3000,*"
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url = f"{URL_BASE}{endpoint}?{query}"
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(len(result_data["obs"]), 38)
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def test_data_json_put(self):
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for axis in ["obs", "var"]:
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endpoint = f"data/{axis}"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/json"}
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obs_filter = {
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"filter": {
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"obs": {
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"annotation_value": [
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{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
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{"name": "n_counts", "min": 3000},
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],
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"index": [1, 99, [1000, 2000]],
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}
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}
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}
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result = self.session.put(url, headers=header, json=obs_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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self.assertEqual(len(result_data["obs"]), 15)
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def test_fbs_default(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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result = self.session.put(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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def test_data_put_fbs(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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result = self.session.put(url, headers=header)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
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df = decode_fbs.decode_matrix_FBS(result.content)
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self.assertEqual(df['n_rows'], 2638)
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self.assertEqual(df['n_cols'], 1838)
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self.assertIsNotNone(df['columns'])
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self.assertListEqual(df['col_idx'].tolist(), [])
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self.assertIsNone(df['row_idx'])
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self.assertEqual(len(df['columns']), df['n_cols'])
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def test_data_put_filter_fbs(self):
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/octet-stream"}
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@@ -384,94 +241,16 @@ class EndPoints(unittest.TestCase):
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self.assertListEqual(df['col_idx'].tolist(), [0, 1, 4])
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def test_data_put_single_var(self):
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for axis in ["obs", "var"]:
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endpoint = f"data/{axis}"
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url = f"{URL_BASE}{endpoint}"
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header = {"Accept": "application/json"}
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var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
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result = self.session.put(url, headers=header, json=var_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data = result.json()
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if axis == "obs":
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self.assertEqual(len(result_data["obs"][0]), 2)
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self.assertEqual(len(result_data["var"]), 1)
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elif axis == "var":
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self.assertEqual(len(result_data["obs"]), 2638)
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self.assertEqual(len(result_data["var"][0]), 2639)
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def test_cache(self):
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endpoint = "annotations/var"
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endpoint = f"data/var"
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url = f"{URL_BASE}{endpoint}"
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f1 = {
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"filter": {
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"var": {
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"annotation_value": [
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{
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"name": "name",
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"values": [
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"HLA-DRB1",
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"HLA-DQA1",
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"HLA-DQB1",
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"HLA-DPA1",
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"HLA-DPB1",
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"MS4A1",
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"IL32",
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"CCL5",
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"CD79B",
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"CD79A",
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],
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}
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]
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}
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}
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}
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result = self.session.put(url, json=f1)
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header = {"Accept": "application/octet-stream"}
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var_filter = {"filter": {"var": {"annotation_value": [{"name": "name", "values": ["RER1"]}]}}}
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result = self.session.put(url, headers=header, json=var_filter)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data1 = result.json()
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f2 = {
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"filter": {
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"var": {
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"annotation_value": [
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{
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"name": "name",
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"values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH", "CCL5", "CCL4", "CST7", "NKG7"],
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}
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]
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}
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}
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}
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result = self.session.put(url, json=f2)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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self.assertEqual(result.headers["Content-Type"], "application/json")
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result_data2 = result.json()
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self.assertNotEqual(result_data1, result_data2)
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def test_cache_nofilter(self):
|
||||
endpoint = "annotations/var"
|
||||
url = f"{URL_BASE}{endpoint}"
|
||||
f1 = {"filter": {}}
|
||||
result = self.session.put(url, json=f1)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
result_data1 = result.json()
|
||||
f2 = {
|
||||
"filter": {
|
||||
"var": {
|
||||
"annotation_value": [
|
||||
{
|
||||
"name": "name",
|
||||
"values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH", "CCL5", "CCL4", "CST7", "NKG7"],
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
result = self.session.put(url, json=f2)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/json")
|
||||
result_data2 = result.json()
|
||||
self.assertNotEqual(result_data1, result_data2)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
|
||||
def test_static(self):
|
||||
endpoint = "static"
|
||||
|
||||
Reference in New Issue
Block a user