mirror of
https://github.com/chanzuckerberg/cellxgene.git
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bmccandless
342a9d774c
* app config bug fix: When reading a config file that included per_dataset_config, the dataroot specializations were applied, but not the default config. This PR fixes that and also includes a test for this case.
199 lines
8.8 KiB
Python
199 lines
8.8 KiB
Python
import os
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import unittest
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from unittest import mock
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from unittest.mock import patch
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import tempfile
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import requests
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from server.common.app_config import AppConfig
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from server.common.errors import ConfigurationError
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from server.common.utils.utils import find_available_port
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from server.test import PROJECT_ROOT, test_server, FIXTURES_ROOT
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# NOTE, there are more tests that should be written for AppConfig.
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# this is just a start.
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def mockenv(**envvars):
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return mock.patch.dict(os.environ, envvars)
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class AppConfigTest(unittest.TestCase):
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def test_update(self):
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config = AppConfig()
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config.update_server_config(app__verbose=True, multi_dataset__dataroot="datadir")
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vars = config.server_config.changes_from_default()
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self.assertCountEqual(vars, [("app__verbose", True, False), ("multi_dataset__dataroot", "datadir", None)])
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config = AppConfig()
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config.update_default_dataset_config(app__scripts=(), app__inline_scripts=())
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vars = config.server_config.changes_from_default()
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self.assertCountEqual(vars, [])
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config = AppConfig()
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config.update_default_dataset_config(app__scripts=[], app__inline_scripts=[])
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vars = config.default_dataset_config.changes_from_default()
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self.assertCountEqual(vars, [])
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config = AppConfig()
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config.update_default_dataset_config(app__scripts=("a", "b"), app__inline_scripts=["c", "d"])
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vars = config.default_dataset_config.changes_from_default()
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self.assertCountEqual(vars, [("app__scripts", ["a", "b"], []), ("app__inline_scripts", ["c", "d"], [])])
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def test_multi_dataset(self):
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config = AppConfig()
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# test for illegal url_dataroots
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for illegal in ("../b", "!$*", "\\n", "", "(bad)"):
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config.update_server_config(
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multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
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)
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with self.assertRaises(ConfigurationError):
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config.complete_config()
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# test for legal url_dataroots
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for legal in ("d", "this.is-okay_", "a/b"):
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config.update_server_config(
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multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
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)
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config.complete_config()
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# test that multi dataroots work end to end
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config.update_server_config(
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multi_dataset__dataroot=dict(
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s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"),
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s2=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set2"),
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s3=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set3"),
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)
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)
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# Change this default to test if the dataroot overrides below work.
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config.update_default_dataset_config(app__about_legal_tos="tos_default.html")
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# specialize the configs for set1
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config.add_dataroot_config(
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"s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html"
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)
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# specialize the configs for set2
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config.add_dataroot_config(
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"s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html"
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)
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# no specializations for set3 (they get the default dataset config)
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config.complete_config()
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with test_server(app_config=config) as server:
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session = requests.Session()
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response = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config")
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data_config = response.json()
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assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
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assert data_config["config"]["parameters"]["annotations"] is False
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assert data_config["config"]["parameters"]["disable-diffexp"] is False
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assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html"
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response = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config")
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data_config = response.json()
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assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
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assert data_config["config"]["parameters"]["annotations"] is True
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assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html"
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response = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config")
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data_config = response.json()
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assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
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assert data_config["config"]["parameters"]["annotations"] is True
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assert data_config["config"]["parameters"]["disable-diffexp"] is False
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assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html"
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response = session.get(f"{server}/health")
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assert response.json()["status"] == "pass"
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@mockenv(CXG_AWS_SECRET_NAME="TESTING", CXG_AWS_SECRET_REGION_NAME="TEST_REGION")
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@patch('server.common.aws_secret_utils.get_secret_key')
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def test_get_config_vars_from_aws_secrets(self, mock_get_secret_key):
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mock_get_secret_key.return_value = {
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"flask_secret_key": "mock_flask_secret",
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"oauth_client_secret": "mock_oauth_secret",
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"db_uri": "mock_db_uri"
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}
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config = AppConfig()
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with self.assertLogs(level="INFO") as logger:
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from server.common.aws_secret_utils import handle_config_from_secret
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# should not throw error
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# "AttributeError: 'XConfig' object has no attribute 'x'"
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handle_config_from_secret(config)
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# should log 3 lines (one for each var set from a secret)
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self.assertEqual(len(logger.output), 3)
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self.assertIn('INFO:root:set app__flask_secret_key from secret', logger.output[0])
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self.assertIn('INFO:root:set authentication__params_oauth__client_secret from secret', logger.output[1])
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self.assertIn('INFO:root:set user_annotations__hosted_tiledb_array__db_uri from secret', logger.output[2])
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self.assertEqual(config.server_config.app__flask_secret_key, "mock_flask_secret")
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self.assertEqual(config.server_config.authentication__params_oauth__client_secret, "mock_oauth_secret")
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self.assertEqual(config.default_dataset_config.user_annotations__hosted_tiledb_array__db_uri, "mock_db_uri")
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def test_api_base_url(self):
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# test the api_base_url feature, and that it can contain a path
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config = AppConfig()
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backend_port = find_available_port("localhost", 10000)
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config.update_server_config(
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app__api_base_url=f"http://localhost:{backend_port}/additional/path/before/dataroot",
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multi_dataset__dataroot=f"{PROJECT_ROOT}/example-dataset"
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)
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config.complete_config()
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with test_server(["-p", str(backend_port)], app_config=config) as server:
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session = requests.Session()
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self.assertEqual(server, f"http://localhost:{backend_port}")
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response = session.get(f"{server}/additional/path/before/dataroot/d/pbmc3k.h5ad/api/v0.2/config")
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self.assertEqual(response.status_code, 200)
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data_config = response.json()
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self.assertEqual(data_config["config"]["displayNames"]["dataset"], "pbmc3k")
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def test_configfile_with_specialization(self):
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# test that per_dataset_config config load the default config, then the specialized config
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with tempfile.TemporaryDirectory() as tempdir:
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configfile = os.path.join(tempdir, "config.yaml")
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with open(configfile, "w") as fconfig:
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config = """
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server:
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multi_dataset:
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dataroot:
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test:
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base_url: test
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dataroot: fake_dataroot
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dataset:
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user_annotations:
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enable: false
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type: hosted_tiledb_array
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hosted_tiledb_array:
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db_uri: fake_db_uri
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hosted_file_directory: fake_dir
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per_dataset_config:
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test:
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user_annotations:
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enable: true
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"""
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fconfig.write(config)
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app_config = AppConfig()
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app_config.update_from_config_file(configfile)
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test_config = app_config.dataroot_config["test"]
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# test config from default
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self.assertEqual(test_config.user_annotations__type, "hosted_tiledb_array")
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self.assertEqual(test_config.user_annotations__hosted_tiledb_array__db_uri, "fake_db_uri")
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# test config from specialization
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self.assertTrue(test_config.user_annotations__enable)
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