mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-01 01:38:12 +08:00
Add user-generated annotations tests to the server (#1164)
* Add user-generated annotations tests to the server Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969 * Auto-format python code * @skip_if: passing lambdas > than property strings * Respond to feedback from @bkmartinjr
This commit is contained in:
Matt Weiden
+181
-40
@@ -1,17 +1,24 @@
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import shutil
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import time
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import unittest
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from http import HTTPStatus
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from subprocess import Popen
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import unittest
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import time
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import pandas as pd
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import requests
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import decode_fbs
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import server.test.decode_fbs as decode_fbs
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from server.test import skip_if, data_with_tmp_annotations, make_fbs
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from server.data_common.matrix_loader import MatrixDataType
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BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
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# TODO (mweiden): remove ANNOTATIONS_ENABLED and Annotation subclasses when annotations are no longer experimental
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# TODO (mweiden): remove MATRIX_DATA_TYPE and skip_if when user annotations for the CXG format is complete
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class EndPoints(object):
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ANNOTATIONS_ENABLED = False
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def setUp(self):
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self.session = requests.Session()
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@@ -25,7 +32,9 @@ class EndPoints(object):
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result_data = result.json()
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self.assertEqual(result_data["schema"]["dataframe"]["nObs"], 2638)
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self.assertEqual(len(result_data["schema"]["annotations"]["obs"]), 2)
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self.assertEqual(len(result_data["schema"]["annotations"]["obs"]["columns"]), 5)
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self.assertEqual(
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len(result_data["schema"]["annotations"]["obs"]["columns"]), 6 if self.ANNOTATIONS_ENABLED else 5
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)
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def test_config(self):
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endpoint = "config"
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@@ -51,7 +60,7 @@ class EndPoints(object):
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self.assertIsNotNone(df["columns"])
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self.assertSetEqual(
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set(df["col_idx"]),
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set(["pca_0", "pca_1", "tsne_0", "tsne_1", "umap_0", "umap_1", "draw_graph_fr_0", "draw_graph_fr_1"]),
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{"pca_0", "pca_1", "tsne_0", "tsne_1", "umap_0", "umap_1", "draw_graph_fr_0", "draw_graph_fr_1"},
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)
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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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@@ -71,14 +80,21 @@ class EndPoints(object):
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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"], 5)
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self.assertEqual(df["n_cols"], 6 if self.ANNOTATIONS_ENABLED else 5)
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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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obs_index_col_name = self.schema["schema"]["annotations"]["obs"]["index"]
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self.assertListEqual(df["col_idx"], [obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"])
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self.assertListEqual(
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df["col_idx"],
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[obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"]
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+ (["cluster-test"] if self.ANNOTATIONS_ENABLED else []),
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)
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@skip_if(
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lambda slf: hasattr(slf, "MATRIX_DATA_TYPE") and slf.MATRIX_DATA_TYPE == MatrixDataType.CXG,
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"CXG file annotations are not feature-complete!",
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)
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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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@@ -91,7 +107,6 @@ class EndPoints(object):
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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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@@ -144,7 +159,6 @@ class EndPoints(object):
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self.assertEqual(df["n_rows"], 1838)
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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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var_index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
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@@ -162,7 +176,6 @@ class EndPoints(object):
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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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@@ -215,7 +228,6 @@ class EndPoints(object):
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self.assertEqual(df["n_rows"], 2638)
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self.assertEqual(df["n_cols"], 3)
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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"].tolist(), [0, 1, 4])
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@@ -240,6 +252,77 @@ class EndPoints(object):
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result = self.session.get(url)
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self.assertEqual(result.status_code, HTTPStatus.OK)
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@staticmethod
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def _setUpClass(child_class, start_command):
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child_class.ps = Popen(start_command)
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child_class.session = requests.Session()
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for i in range(90):
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try:
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result = child_class.session.get(f"{child_class.URL_BASE}schema")
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child_class.schema = result.json()
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except requests.exceptions.ConnectionError:
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time.sleep(1)
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@staticmethod
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def _tearDownClass(child_class):
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try:
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child_class.ps.terminate()
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except ProcessLookupError:
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pass
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class EndPointsAnnotations(EndPoints):
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def test_get_schema_existing_writable(self):
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self._test_get_schema_writable("cluster-test")
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@skip_if(lambda slf: slf.MATRIX_DATA_TYPE == MatrixDataType.CXG, "CXG file annotations are not feature-complete!")
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def test_get_user_annotations_existing_obs_keys_fbs(self):
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self._test_get_user_annotations_obs_keys_fbs(
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"cluster-test", {"unassigned", "one", "two", "three", "four", "five"},
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)
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@skip_if(lambda slf: slf.MATRIX_DATA_TYPE == MatrixDataType.CXG, "CXG file annotations are not feature-complete!")
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def test_put_user_annotations_obs_fbs(self):
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endpoint = "annotations/obs"
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query = "annotation-collection-name=test_annotations"
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url = f"{self.URL_BASE}{endpoint}?{query}"
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n_rows = self.data.get_shape()[0]
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fbs = make_fbs({"cat_A": pd.Series(["label_A" for l in range(0, n_rows)], dtype="category")})
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result = self.session.put(url, data=fbs)
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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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self.assertEqual(result.json(), {"status": "OK"})
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self._test_get_schema_writable("cat_A")
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self._test_get_user_annotations_obs_keys_fbs("cat_A", {"label_A"})
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def _test_get_user_annotations_obs_keys_fbs(self, annotation_name, columns):
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endpoint = "annotations/obs"
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query = f"annotation-name={annotation_name}"
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url = f"{self.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"], 1)
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self.assertListEqual(df["col_idx"], [annotation_name])
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self.assertEqual(set(df["columns"][0]), columns)
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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_get_schema_writable(self, cluster_name):
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endpoint = "schema"
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url = f"{self.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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columns = result_data["schema"]["annotations"]["obs"]["columns"]
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matching_columns = [c for c in columns if c["name"] == cluster_name]
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self.assertEqual(len(matching_columns), 1)
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self.assertTrue(matching_columns[0]["writable"])
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class EndPointsAnndata(unittest.TestCase, EndPoints):
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"""Test Case for endpoints"""
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@@ -251,7 +334,8 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
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@classmethod
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def setUpClass(cls):
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cls.ps = Popen(
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cls._setUpClass(
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cls,
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[
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"cellxgene",
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"--no-upgrade-check",
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@@ -260,22 +344,16 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
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"--verbose",
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"--port",
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str(cls.PORT),
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]
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],
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)
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cls.session = requests.Session()
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for i in range(90):
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try:
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result = cls.session.get(f"{cls.URL_BASE}schema")
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cls.schema = result.json()
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except requests.exceptions.ConnectionError:
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time.sleep(1)
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@classmethod
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def tearDownClass(cls):
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try:
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cls.ps.terminate()
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except ProcessLookupError:
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pass
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cls._tearDownClass(cls)
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@property
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def annotations_enabled(self):
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return False
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class EndPointsCxg(unittest.TestCase, EndPoints):
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@@ -288,28 +366,91 @@ class EndPointsCxg(unittest.TestCase, EndPoints):
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@classmethod
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def setUpClass(cls):
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cls.ps = Popen(
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cls._setUpClass(
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cls,
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[
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"cellxgene",
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"--no-upgrade-check",
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"launch",
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"../example-dataset/pbmc3k.cxg",
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"test/test_datasets/pbmc3k.cxg",
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"--verbose",
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"--port",
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str(cls.PORT),
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]
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],
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)
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cls.session = requests.Session()
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for i in range(90):
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try:
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result = cls.session.get(f"{cls.URL_BASE}schema")
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cls.schema = result.json()
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except requests.exceptions.ConnectionError:
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time.sleep(1)
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@classmethod
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def tearDownClass(cls):
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try:
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cls.ps.terminate()
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except ProcessLookupError:
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pass
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cls._tearDownClass(cls)
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class EndPointsAnndataAnnotations(unittest.TestCase, EndPointsAnnotations):
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"""Test Case for endpoints"""
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PORT = 5012
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LOCAL_URL = f"http://127.0.0.1:{PORT}/"
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VERSION = "v0.2"
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URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
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ANNOTATIONS_ENABLED = True
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MATRIX_DATA_TYPE = MatrixDataType.H5AD
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@classmethod
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def setUpClass(cls):
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cls.data, cls.tmp_dir, cls.annotations = data_with_tmp_annotations(
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MatrixDataType.H5AD, annotations_fixture=True
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)
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cls._setUpClass(
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cls,
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[
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"cellxgene",
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"--no-upgrade-check",
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"launch",
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"--experimental-annotations",
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"--experimental-annotations-file",
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cls.annotations.output_file,
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"--verbose",
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"--port",
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str(cls.PORT),
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cls.data.get_location(),
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],
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)
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@classmethod
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def tearDownClass(cls):
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shutil.rmtree(cls.tmp_dir)
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cls._tearDownClass(cls)
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class EndPointsCxgAnnotations(unittest.TestCase, EndPointsAnnotations):
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"""Test Case for endpoints"""
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PORT = 5013
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LOCAL_URL = f"http://127.0.0.1:{PORT}/"
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VERSION = "v0.2"
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URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
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ANNOTATIONS_ENABLED = True
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MATRIX_DATA_TYPE = MatrixDataType.CXG
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@classmethod
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def setUpClass(cls):
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cls.data, cls.tmp_dir, cls.annotations = data_with_tmp_annotations(MatrixDataType.CXG, annotations_fixture=True)
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cls._setUpClass(
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cls,
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[
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"cellxgene",
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"--no-upgrade-check",
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"launch",
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"--experimental-annotations",
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"--experimental-annotations-file",
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cls.annotations.output_file,
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"--verbose",
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"--port",
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str(cls.PORT),
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cls.data.get_location(),
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],
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)
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@classmethod
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def tearDownClass(cls):
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shutil.rmtree(cls.tmp_dir)
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cls._tearDownClass(cls)
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