mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-03 02:28:12 +08:00
config refactor (#1854)
* split out config * add tests for base and app config, refactor client config out of app config * refactor default config retrieval * create config test class and helper functions * move default_config into server to fix import issue
This commit is contained in:
Madison Dunitz
@@ -0,0 +1,246 @@
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import os
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import shutil
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import unittest
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import random
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from unittest import mock
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from server.test import FIXTURES_ROOT
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def mockenv(**envvars):
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return mock.patch.dict(os.environ, envvars)
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class ConfigTests(unittest.TestCase):
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tmp_fixtures_directory = os.path.join(FIXTURES_ROOT, "tmp_dir")
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@classmethod
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def tearDownClass(cls) -> None:
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shutil.rmtree(cls.tmp_fixtures_directory)
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@classmethod
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def setUpClass(cls) -> None:
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os.makedirs(cls.tmp_fixtures_directory)
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def custom_server_config(
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self,
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verbose="false",
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debug="false",
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host="localhost",
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port="null",
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open_browser="false",
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force_https="false",
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flask_secret_key="null",
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generate_cache_control_headers="false",
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server_timing_headers="false",
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csp_directives="null",
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api_base_url="null",
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web_base_url="null",
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auth_type="session",
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oauth_api_base_url="null",
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client_id="null",
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client_secret="null",
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jwt_decode_options="null",
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session_cookie="true",
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cookie="null",
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dataroot="null",
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index="false",
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allowed_matrix_types=[],
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max_cached_datasets=5,
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timelimit_s=5,
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dataset_datapath="null",
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obs_names="null",
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var_names="null",
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about="null",
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title="null",
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diffexp_max_workers=64,
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cpu_multiplier=4,
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target_workunit="16_000_000",
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data_locater_region_name="us-east-1",
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cxg_tile_cache_size=8589934592,
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cxg_num_reader_threads=32,
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anndata_backed="false",
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column_request_max=32,
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diffexp_cellcount_max="null",
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config_file_name="server_config.yaml",
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):
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configfile = os.path.join(self.tmp_fixtures_directory, config_file_name)
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server_config_outline_path = os.path.join(FIXTURES_ROOT, "server_config_outline.py")
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with open(server_config_outline_path, "r") as config_skeleton:
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config = config_skeleton.read()
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server_config = eval(config)
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with open(configfile, "w") as server_config_file:
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server_config_file.write(server_config)
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return configfile
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def custom_app_config(
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self,
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verbose="false",
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debug="false",
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host="localhost",
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port="null",
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open_browser="false",
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force_https="false",
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flask_secret_key="null",
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generate_cache_control_headers="false",
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server_timing_headers="false",
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csp_directives="null",
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api_base_url="null",
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web_base_url="null",
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auth_type="session",
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oauth_api_base_url="null",
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client_id="null",
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client_secret="null",
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jwt_decode_options="null",
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session_cookie="true",
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cookie="null",
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dataroot="null",
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index="false",
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allowed_matrix_types=[],
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max_cached_datasets=5,
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timelimit_s=5,
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dataset_datapath="null",
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obs_names="null",
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var_names="null",
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about="null",
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title="null",
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diffexp_max_workers=64,
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cpu_multiplier=4,
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target_workunit="16_000_000",
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data_locater_region_name="us-east-1",
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cxg_tile_cache_size=8589934592,
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cxg_num_reader_threads=32,
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anndata_backed="false",
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column_request_max=32,
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diffexp_cellcount_max="null",
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scripts=[],
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inline_scripts=[],
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about_legal_tos="null",
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about_legal_privacy="null",
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authentication_enable="true",
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max_categories=1000,
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custom_colors="true",
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enable_users_annotations="true",
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annotation_type="local_file_csv",
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db_uri="null",
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hosted_file_directory="null",
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local_file_csv_directory="null",
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local_file_csv_file="null",
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ontology_enabled="false",
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obo_location="null",
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embedding_names=[],
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enable_reembedding="false",
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enable_difexp="true",
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lfc_cutoff=0.01,
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top_n=10,
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config_file_name="app_config.yml",
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):
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random_num = random.randrange(999999)
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configfile = os.path.join(self.tmp_fixtures_directory, config_file_name)
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server_config = self.custom_server_config(
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verbose=verbose,
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debug=debug,
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host=host,
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port=port,
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open_browser=open_browser,
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force_https=force_https,
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flask_secret_key=flask_secret_key,
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generate_cache_control_headers=generate_cache_control_headers,
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server_timing_headers=server_timing_headers,
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csp_directives=csp_directives,
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api_base_url=api_base_url,
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web_base_url=web_base_url,
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auth_type=auth_type,
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oauth_api_base_url=oauth_api_base_url,
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client_id=client_id,
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client_secret=client_secret,
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jwt_decode_options=jwt_decode_options,
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session_cookie=session_cookie,
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cookie=cookie,
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dataroot=dataroot,
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index=index,
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allowed_matrix_types=allowed_matrix_types,
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max_cached_datasets=max_cached_datasets,
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timelimit_s=timelimit_s,
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dataset_datapath=dataset_datapath,
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obs_names=obs_names,
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var_names=var_names,
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about=about,
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title=title,
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diffexp_max_workers=diffexp_max_workers,
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cpu_multiplier=cpu_multiplier,
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target_workunit=target_workunit,
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data_locater_region_name=data_locater_region_name,
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cxg_tile_cache_size=cxg_tile_cache_size,
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cxg_num_reader_threads=cxg_num_reader_threads,
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anndata_backed=anndata_backed,
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column_request_max=column_request_max,
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diffexp_cellcount_max=diffexp_cellcount_max,
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config_file_name=f"temp_server_config_{random_num}.yml",
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)
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dataset_config = self.custom_dataset_config(
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scripts=scripts,
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inline_scripts=inline_scripts,
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about_legal_tos=about_legal_tos,
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about_legal_privacy=about_legal_privacy,
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authentication_enable=authentication_enable,
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max_categories=max_categories,
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custom_colors=custom_colors,
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enable_users_annotations=enable_users_annotations,
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annotation_type=annotation_type,
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db_uri=db_uri,
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hosted_file_directory=hosted_file_directory,
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local_file_csv_directory=local_file_csv_directory,
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local_file_csv_file=local_file_csv_file,
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ontology_enabled=ontology_enabled,
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obo_location=obo_location,
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embedding_names=embedding_names,
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enable_reembedding=enable_reembedding,
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enable_difexp=enable_difexp,
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lfc_cutoff=lfc_cutoff,
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top_n=top_n,
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config_file_name=f"temp_dataset_config_{random_num}.yml",
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)
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with open(server_config) as server_config:
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with open(dataset_config) as dataset_config:
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with open(configfile, "w") as app_config_file:
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for line in server_config:
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app_config_file.write(line)
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for line in dataset_config:
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app_config_file.write(line)
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return configfile
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def custom_dataset_config(
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self,
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scripts=[],
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inline_scripts=[],
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about_legal_tos="null",
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about_legal_privacy="null",
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authentication_enable="true",
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max_categories=1000,
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custom_colors="true",
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enable_users_annotations="true",
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annotation_type="local_file_csv",
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db_uri="null",
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hosted_file_directory="null",
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local_file_csv_directory="null",
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local_file_csv_file="null",
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ontology_enabled="false",
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obo_location="null",
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embedding_names=[],
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enable_reembedding="false",
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enable_difexp="true",
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lfc_cutoff=0.01,
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top_n=10,
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config_file_name="dataset_config.yml",
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):
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configfile = os.path.join(self.tmp_fixtures_directory, config_file_name)
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dataset_config_outline_path = os.path.join(FIXTURES_ROOT, "dataset_config_outline.py")
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with open(dataset_config_outline_path, "r") as config_skeleton:
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config = config_skeleton.read()
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dataset_config = eval(config)
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with open(configfile, "w") as dataset_config_file:
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dataset_config_file.write(dataset_config)
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return configfile
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@@ -0,0 +1,140 @@
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import os
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import tempfile
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import unittest
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import yaml
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from server.default_config import default_config
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from server.common.config.app_config import AppConfig
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from server.test.unit.common.config import ConfigTests
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from server.common.errors import ConfigurationError
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from server.test import FIXTURES_ROOT
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class AppConfigTest(ConfigTests):
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def setUp(self):
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self.config_file_name = f"{unittest.TestCase.id(self).split('.')[-1]}.yml"
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self.config = AppConfig()
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self.config.update_server_config(multi_dataset__dataroot=FIXTURES_ROOT)
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self.server_config = self.config.server_config
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self.config.complete_config()
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message_list = []
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def noop(message):
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message_list.append(message)
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messagefn = noop
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self.context = dict(messagefn=messagefn, messages=message_list)
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def get_config(self, **kwargs):
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file_name = self.custom_app_config(
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dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs
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)
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config = AppConfig()
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config.update_from_config_file(file_name)
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return config
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def test_get_default_config_correctly_reads_default_config_file(self):
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app_default_config = AppConfig().default_config
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expected_config = yaml.load(default_config, Loader=yaml.Loader)
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server_config = app_default_config['server']
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dataset_config = app_default_config['dataset']
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expected_server_config = expected_config['server']
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expected_dataset_config = expected_config['dataset']
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self.assertDictEqual(app_default_config, expected_config)
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self.assertDictEqual(server_config, expected_server_config)
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self.assertDictEqual(dataset_config, expected_dataset_config)
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def test_get_dataset_config_returns_default_dataset_config_for_single_datasets(self):
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datapath = f"{FIXTURES_ROOT}/1e4dfec4-c0b2-46ad-a04e-ff3ffb3c0a8f.h5ad"
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file_name = self.custom_app_config(dataset_datapath=datapath, config_file_name=self.config_file_name)
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config = AppConfig()
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config.update_from_config_file(file_name)
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self.assertEqual(config.get_dataset_config(""), config.default_dataset_config)
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def test_update_server_config_updates_server_config_and_config_status(self):
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config = self.get_config()
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config.complete_config()
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config.check_config()
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config.update_server_config(multi_dataset__dataroot=FIXTURES_ROOT)
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with self.assertRaises(ConfigurationError):
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config.server_config.check_config()
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def test_write_config_outputs_yaml_with_all_config_vars(self):
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config = self.get_config()
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config.write_config(f"{FIXTURES_ROOT}/tmp_dir/write_config.yml")
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with open(f"{FIXTURES_ROOT}/tmp_dir/{self.config_file_name}", "r") as default_config:
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default_config_yml = yaml.safe_load(default_config)
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with open(f"{FIXTURES_ROOT}/tmp_dir/write_config.yml", "r") as output_config:
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output_config_yml = yaml.safe_load(output_config)
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self.maxDiff = None
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self.assertEqual(default_config_yml, output_config_yml)
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def test_update_app_config(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_configfile_no_dataset_section(self):
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# test a config file without a dataset section
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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: test_dataroot
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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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server_changes = app_config.server_config.changes_from_default()
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dataset_changes = app_config.default_dataset_config.changes_from_default()
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self.assertEqual(server_changes, [("multi_dataset__dataroot", "test_dataroot", None)])
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self.assertEqual(dataset_changes, [])
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def test_configfile_no_server_section(self):
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# test a config file without a dataset section
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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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dataset:
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user_annotations:
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enable: false
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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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server_changes = app_config.server_config.changes_from_default()
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dataset_changes = app_config.default_dataset_config.changes_from_default()
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self.assertEqual(server_changes, [])
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self.assertEqual(dataset_changes, [("user_annotations__enable", False, True)])
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@@ -0,0 +1,63 @@
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import unittest
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from server.common.config.app_config import AppConfig
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from server.test import FIXTURES_ROOT
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from server.test.unit.common.config import ConfigTests
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from server.common.errors import ConfigurationError
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class BaseConfigTest(ConfigTests):
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def setUp(self):
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self.config_file_name = f"{unittest.TestCase.id(self).split('.')[-1]}.yml"
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self.config = AppConfig()
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self.config.update_server_config(multi_dataset__dataroot=FIXTURES_ROOT)
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self.server_config = self.config.server_config
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self.config.complete_config()
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message_list = []
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def noop(message):
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message_list.append(message)
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messagefn = noop
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self.context = dict(messagefn=messagefn, messages=message_list)
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def get_config(self, **kwargs):
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file_name = self.custom_app_config(
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dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs
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)
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config = AppConfig()
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config.update_from_config_file(file_name)
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return config
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def test_mapping_creation_returns_map_of_server_and_dataset_config(self):
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config = AppConfig()
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mapping = config.default_dataset_config.create_mapping(config.default_config)
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self.assertIsNotNone(mapping["server__app__verbose"])
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self.assertIsNotNone(mapping["dataset__presentation__max_categories"])
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self.assertIsNotNone(mapping["dataset__user_annotations__ontology__obo_location"])
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self.assertIsNotNone(mapping["server__multi_dataset__allowed_matrix_types"])
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def test_changes_from_default_returns_list_of_nondefault_config_values(self):
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config = self.get_config(verbose="true", lfc_cutoff=0.05)
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server_changes = config.server_config.changes_from_default()
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dataset_changes = config.default_dataset_config.changes_from_default()
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self.assertEqual(
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server_changes,
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[
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("app__verbose", True, False),
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("multi_dataset__dataroot", FIXTURES_ROOT, None),
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("multi_dataset__matrix_cache__timelimit_s", 5, 30),
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("data_locator__s3__region_name", "us-east-1", True),
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],
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)
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||||
self.assertEqual(dataset_changes, [("diffexp__lfc_cutoff", 0.05, 0.01)])
|
||||
|
||||
def test_check_config_throws_error_if_attr_has_not_been_checked(self):
|
||||
config = self.get_config(verbose="true")
|
||||
config.complete_config()
|
||||
config.check_config()
|
||||
config.update_server_config(app__verbose=False)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.check_config()
|
||||
@@ -0,0 +1,260 @@
|
||||
import os
|
||||
import tempfile
|
||||
|
||||
import requests
|
||||
import unittest
|
||||
from unittest.mock import patch
|
||||
|
||||
from server.common.annotations.hosted_tiledb import AnnotationsHostedTileDB
|
||||
from server.common.annotations.local_file_csv import AnnotationsLocalFile
|
||||
from server.common.config.app_config import AppConfig
|
||||
from server.common.config.base_config import BaseConfig
|
||||
from server.test import test_server, PROJECT_ROOT, FIXTURES_ROOT
|
||||
|
||||
from server.common.errors import ConfigurationError
|
||||
from server.test.unit.common.config import ConfigTests
|
||||
|
||||
|
||||
class TestDatasetConfig(ConfigTests):
|
||||
def setUp(self):
|
||||
self.config_file_name = f"{unittest.TestCase.id(self).split('.')[-1]}.yml"
|
||||
self.config = AppConfig()
|
||||
self.config.update_server_config(multi_dataset__dataroot=FIXTURES_ROOT)
|
||||
self.dataset_config = self.config.default_dataset_config
|
||||
self.config.complete_config()
|
||||
message_list = []
|
||||
|
||||
def noop(message):
|
||||
message_list.append(message)
|
||||
|
||||
messagefn = noop
|
||||
self.context = dict(messagefn=messagefn, messages=message_list)
|
||||
|
||||
def get_config(self, **kwargs):
|
||||
file_name = self.custom_app_config(
|
||||
dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
return config
|
||||
|
||||
def test_init_datatset_config_sets_vars_from_default_config(self):
|
||||
config = AppConfig()
|
||||
self.assertEqual(config.default_dataset_config.presentation__max_categories, 1000)
|
||||
self.assertEqual(config.default_dataset_config.user_annotations__type, "local_file_csv")
|
||||
self.assertEqual(config.default_dataset_config.diffexp__lfc_cutoff, 0.01)
|
||||
self.assertIsNone(config.default_dataset_config.user_annotations__ontology__obo_location)
|
||||
|
||||
@patch("server.common.config.dataset_config.BaseConfig.validate_correct_type_of_configuration_attribute")
|
||||
def test_complete_config_checks_all_attr(self, mock_check_attrs):
|
||||
mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
|
||||
self.dataset_config.complete_config(self.context)
|
||||
self.assertEqual(mock_check_attrs.call_count, 21)
|
||||
|
||||
def test_app_sets_script_vars(self):
|
||||
config = self.get_config(scripts=["path/to/script"])
|
||||
config.default_dataset_config.handle_app()
|
||||
|
||||
self.assertEqual(config.default_dataset_config.app__scripts, [{"src": "path/to/script"}])
|
||||
|
||||
config = self.get_config(scripts=[{"src": "path/to/script", "more": "different/script/path"}])
|
||||
config.default_dataset_config.handle_app()
|
||||
self.assertEqual(
|
||||
config.default_dataset_config.app__scripts, [{"src": "path/to/script", "more": "different/script/path"}]
|
||||
)
|
||||
|
||||
config = self.get_config(scripts=["path/to/script", "different/script/path"])
|
||||
config.default_dataset_config.handle_app()
|
||||
# TODO @madison -- is this the desired functionality?
|
||||
self.assertEqual(
|
||||
config.default_dataset_config.app__scripts, [{"src": "path/to/script"}, {"src": "different/script/path"}]
|
||||
)
|
||||
|
||||
config = self.get_config(scripts=[{"more": "different/script/path"}])
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.default_dataset_config.handle_app()
|
||||
|
||||
def test_handle_user_annotations_ensures_auth_is_enabled_with_valid_auth_type(self):
|
||||
config = self.get_config(enable_users_annotations="true", authentication_enable="false")
|
||||
config.server_config.complete_config(self.context)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.default_dataset_config.handle_user_annotations(self.context)
|
||||
|
||||
config = self.get_config(enable_users_annotations="true", authentication_enable="true", auth_type="pretend")
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.server_config.complete_config(self.context)
|
||||
|
||||
def test_handle_user_annotations__adds_warning_message_if_annotation_vars_set_when_annotations_disabled(self):
|
||||
config = self.get_config(
|
||||
enable_users_annotations="false", authentication_enable="false", db_uri="shouldnt/be/set"
|
||||
)
|
||||
config.default_dataset_config.handle_user_annotations(self.context)
|
||||
|
||||
self.assertEqual(self.context["messages"], ["Warning: db_uri ignored as annotations are disabled."])
|
||||
|
||||
@patch("server.common.config.dataset_config.DbUtils")
|
||||
def test_handle_user_annotations__instantiates_user_annotations_class_correctly(self, mock_db_utils):
|
||||
mock_db_utils.return_value = "123"
|
||||
config = self.get_config(
|
||||
enable_users_annotations="true", authentication_enable="true", annotation_type="local_file_csv"
|
||||
)
|
||||
config.server_config.complete_config(self.context)
|
||||
config.default_dataset_config.handle_user_annotations(self.context)
|
||||
self.assertIsInstance(config.default_dataset_config.user_annotations, AnnotationsLocalFile)
|
||||
|
||||
config = self.get_config(
|
||||
enable_users_annotations="true",
|
||||
authentication_enable="true",
|
||||
annotation_type="hosted_tiledb_array",
|
||||
db_uri="gotta/set/this",
|
||||
hosted_file_directory="and/this",
|
||||
)
|
||||
config.server_config.complete_config(self.context)
|
||||
config.default_dataset_config.handle_user_annotations(self.context)
|
||||
self.assertIsInstance(config.default_dataset_config.user_annotations, AnnotationsHostedTileDB)
|
||||
|
||||
config = self.get_config(
|
||||
enable_users_annotations="true", authentication_enable="true", annotation_type="NOT_REAL"
|
||||
)
|
||||
config.server_config.complete_config(self.context)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.default_dataset_config.handle_user_annotations(self.context)
|
||||
|
||||
def test_handle_local_file_csv_annotations__sets_dir_if_not_passed_in(self):
|
||||
config = self.get_config(
|
||||
enable_users_annotations="true", authentication_enable="true", annotation_type="local_file_csv"
|
||||
)
|
||||
config.server_config.complete_config(self.context)
|
||||
config.default_dataset_config.handle_local_file_csv_annotations()
|
||||
self.assertIsInstance(config.default_dataset_config.user_annotations, AnnotationsLocalFile)
|
||||
cwd = os.getcwd()
|
||||
self.assertEqual(config.default_dataset_config.user_annotations._get_output_dir(), cwd)
|
||||
|
||||
def test_handle_embeddings__checks_data_file_types(self):
|
||||
file_name = self.custom_app_config(
|
||||
embedding_names=["name1", "name2"],
|
||||
enable_reembedding="true",
|
||||
dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad",
|
||||
anndata_backed="true",
|
||||
config_file_name=self.config_file_name,
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
config.server_config.complete_config(self.context)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.default_dataset_config.handle_embeddings()
|
||||
|
||||
def test_handle_diffexp__raises_warning_for_large_datasets(self):
|
||||
config = self.get_config(lfc_cutoff=0.02, enable_difexp="true", top_n=15)
|
||||
config.server_config.complete_config(self.context)
|
||||
config.default_dataset_config.handle_diffexp(self.context)
|
||||
self.assertEqual(len(self.context["messages"]), 0)
|
||||
|
||||
def test_multi_dataset(self):
|
||||
config = AppConfig()
|
||||
# test for illegal url_dataroots
|
||||
for illegal in ("../b", "!$*", "\\n", "", "(bad)"):
|
||||
config.update_server_config(
|
||||
multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
|
||||
)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.complete_config()
|
||||
|
||||
# test for legal url_dataroots
|
||||
for legal in ("d", "this.is-okay_", "a/b"):
|
||||
config.update_server_config(
|
||||
multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
|
||||
)
|
||||
config.complete_config()
|
||||
|
||||
# test that multi dataroots work end to end
|
||||
config.update_server_config(
|
||||
multi_dataset__dataroot=dict(
|
||||
s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"),
|
||||
s2=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set2"),
|
||||
s3=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set3"),
|
||||
)
|
||||
)
|
||||
|
||||
# Change this default to test if the dataroot overrides below work.
|
||||
config.update_default_dataset_config(app__about_legal_tos="tos_default.html")
|
||||
|
||||
# specialize the configs for set1
|
||||
config.add_dataroot_config(
|
||||
"s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html"
|
||||
)
|
||||
|
||||
# specialize the configs for set2
|
||||
config.add_dataroot_config(
|
||||
"s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html"
|
||||
)
|
||||
|
||||
# no specializations for set3 (they get the default dataset config)
|
||||
config.complete_config()
|
||||
|
||||
with test_server(app_config=config) as server:
|
||||
session = requests.Session()
|
||||
|
||||
response = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config")
|
||||
data_config = response.json()
|
||||
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
|
||||
assert data_config["config"]["parameters"]["annotations"] is False
|
||||
assert data_config["config"]["parameters"]["disable-diffexp"] is False
|
||||
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html"
|
||||
|
||||
response = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config")
|
||||
data_config = response.json()
|
||||
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
|
||||
assert data_config["config"]["parameters"]["annotations"] is True
|
||||
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html"
|
||||
|
||||
response = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config")
|
||||
data_config = response.json()
|
||||
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
|
||||
assert data_config["config"]["parameters"]["annotations"] is True
|
||||
assert data_config["config"]["parameters"]["disable-diffexp"] is False
|
||||
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html"
|
||||
|
||||
response = session.get(f"{server}/health")
|
||||
assert response.json()["status"] == "pass"
|
||||
|
||||
def test_configfile_with_specialization(self):
|
||||
# test that per_dataset_config config load the default config, then the specialized config
|
||||
|
||||
with tempfile.TemporaryDirectory() as tempdir:
|
||||
configfile = os.path.join(tempdir, "config.yaml")
|
||||
with open(configfile, "w") as fconfig:
|
||||
config = """
|
||||
server:
|
||||
multi_dataset:
|
||||
dataroot:
|
||||
test:
|
||||
base_url: test
|
||||
dataroot: fake_dataroot
|
||||
|
||||
dataset:
|
||||
user_annotations:
|
||||
enable: false
|
||||
type: hosted_tiledb_array
|
||||
hosted_tiledb_array:
|
||||
db_uri: fake_db_uri
|
||||
hosted_file_directory: fake_dir
|
||||
|
||||
per_dataset_config:
|
||||
test:
|
||||
user_annotations:
|
||||
enable: true
|
||||
"""
|
||||
fconfig.write(config)
|
||||
|
||||
app_config = AppConfig()
|
||||
app_config.update_from_config_file(configfile)
|
||||
|
||||
test_config = app_config.dataroot_config["test"]
|
||||
|
||||
# test config from default
|
||||
self.assertEqual(test_config.user_annotations__type, "hosted_tiledb_array")
|
||||
self.assertEqual(test_config.user_annotations__hosted_tiledb_array__db_uri, "fake_db_uri")
|
||||
|
||||
# test config from specialization
|
||||
self.assertTrue(test_config.user_annotations__enable)
|
||||
@@ -0,0 +1,335 @@
|
||||
import os
|
||||
import unittest
|
||||
from unittest import mock
|
||||
from unittest.mock import patch
|
||||
|
||||
from server.common.config.base_config import BaseConfig
|
||||
from server.common.utils.utils import find_available_port
|
||||
from server.test import PROJECT_ROOT, FIXTURES_ROOT
|
||||
|
||||
import requests
|
||||
|
||||
from server.common.config.app_config import AppConfig
|
||||
from server.common.errors import ConfigurationError
|
||||
from server.test import test_server
|
||||
from server.test.unit.common.config import ConfigTests
|
||||
|
||||
|
||||
def mockenv(**envvars):
|
||||
return mock.patch.dict(os.environ, envvars)
|
||||
|
||||
|
||||
class TestServerConfig(ConfigTests):
|
||||
def setUp(self):
|
||||
self.config_file_name = f"{unittest.TestCase.id(self).split('.')[-1]}.yml"
|
||||
self.config = AppConfig()
|
||||
self.config.update_server_config(multi_dataset__dataroot=FIXTURES_ROOT)
|
||||
self.server_config = self.config.server_config
|
||||
self.config.complete_config()
|
||||
|
||||
message_list = []
|
||||
|
||||
def noop(message):
|
||||
message_list.append(message)
|
||||
|
||||
messagefn = noop
|
||||
self.context = dict(messagefn=messagefn, messages=message_list)
|
||||
|
||||
def get_config(self, **kwargs):
|
||||
file_name = self.custom_app_config(
|
||||
dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
return config
|
||||
|
||||
def test_init_raises_error_if_default_config_is_invalid(self):
|
||||
invalid_config = self.get_config(port="not_valid")
|
||||
with self.assertRaises(ConfigurationError):
|
||||
invalid_config.complete_config()
|
||||
|
||||
@patch("server.common.config.server_config.BaseConfig.validate_correct_type_of_configuration_attribute")
|
||||
def test_complete_config_checks_all_attr(self, mock_check_attrs):
|
||||
mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
|
||||
self.server_config.complete_config(self.context)
|
||||
self.assertEqual(mock_check_attrs.call_count, 40)
|
||||
|
||||
def test_handle_app__throws_error_if_port_doesnt_exist(self):
|
||||
config = self.get_config(port=99999999)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.server_config.handle_app(self.context)
|
||||
|
||||
@patch("server.common.config.server_config.discover_s3_region_name")
|
||||
def test_handle_data_locator_works_for_default_types(self, mock_discover_region_name):
|
||||
mock_discover_region_name.return_value = None
|
||||
# Default config
|
||||
self.assertEqual(self.config.server_config.data_locator__s3__region_name, None)
|
||||
# hard coded
|
||||
config = self.get_config()
|
||||
self.assertEqual(config.server_config.data_locator__s3__region_name, "us-east-1")
|
||||
# incorrectly formatted
|
||||
dataroot = {
|
||||
"d1": {"base_url": "set1", "dataroot": "/path/to/set1_datasets/"},
|
||||
"d2": {"base_url": "set2/subdir", "dataroot": "s3://shouldnt/work"},
|
||||
}
|
||||
file_name = self.custom_app_config(
|
||||
dataroot=dataroot, config_file_name=self.config_file_name, data_locater_region_name="true"
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.server_config.handle_data_locator()
|
||||
|
||||
@patch("server.common.config.server_config.discover_s3_region_name")
|
||||
def test_handle_data_locator_can_read_from_dataroot(self, mock_discover_region_name):
|
||||
mock_discover_region_name.return_value = "us-west-2"
|
||||
dataroot = {
|
||||
"d1": {"base_url": "set1", "dataroot": "/path/to/set1_datasets/"},
|
||||
"d2": {"base_url": "set2/subdir", "dataroot": "s3://hosted-cellxgene-dev"},
|
||||
}
|
||||
file_name = self.custom_app_config(
|
||||
dataroot=dataroot, config_file_name=self.config_file_name, data_locater_region_name="true"
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
config.server_config.handle_data_locator()
|
||||
self.assertEqual(config.server_config.data_locator__s3__region_name, "us-west-2")
|
||||
mock_discover_region_name.assert_called_once_with("s3://hosted-cellxgene-dev")
|
||||
|
||||
def test_handle_app___can_use_envar_port(self):
|
||||
config = self.get_config(port=24)
|
||||
self.assertEqual(config.server_config.app__port, 24)
|
||||
|
||||
# Note if the port is set in the config file it will NOT be overwritten by a different envvar
|
||||
os.environ["CXG_SERVER_PORT"] = "4008"
|
||||
self.config = AppConfig()
|
||||
self.config.server_config.handle_app(self.context)
|
||||
self.assertEqual(self.config.server_config.app__port, 4008)
|
||||
|
||||
def test_handle_app__can_get_secret_key_from_envvar_or_config_file_with_envvar_given_preference(self):
|
||||
config = self.get_config(flask_secret_key="KEY_FROM_FILE")
|
||||
self.assertEqual(config.server_config.app__flask_secret_key, "KEY_FROM_FILE")
|
||||
|
||||
os.environ["CXG_SECRET_KEY"] = "KEY_FROM_ENV"
|
||||
config.server_config.handle_app(self.context)
|
||||
self.assertEqual(config.server_config.app__flask_secret_key, "KEY_FROM_ENV")
|
||||
|
||||
def test_handle_app__sets_web_base_url(self):
|
||||
config = self.get_config(web_base_url="anything.com")
|
||||
self.assertEqual(config.server_config.app__web_base_url, "anything.com")
|
||||
|
||||
def test_handle_auth__gets_client_secret_from_envvars_or_config_with_envvars_given_preference(self):
|
||||
config = self.get_config(client_secret="KEY_FROM_FILE")
|
||||
config.server_config.handle_authentication()
|
||||
self.assertEqual(config.server_config.authentication__params_oauth__client_secret, "KEY_FROM_FILE")
|
||||
|
||||
os.environ["CXG_OAUTH_CLIENT_SECRET"] = "KEY_FROM_ENV"
|
||||
config.server_config.handle_authentication()
|
||||
|
||||
self.assertEqual(config.server_config.authentication__params_oauth__client_secret, "KEY_FROM_ENV")
|
||||
|
||||
def test_handle_data_source__errors_when_passed_zero_or_two_dataroots(self):
|
||||
file_name = self.custom_app_config(
|
||||
dataroot=f"{FIXTURES_ROOT}",
|
||||
config_file_name="two_data_roots.yml",
|
||||
dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad",
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.server_config.handle_data_source()
|
||||
|
||||
file_name = self.custom_app_config(config_file_name="zero_roots.yml")
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.server_config.handle_data_source()
|
||||
|
||||
def test_get_api_base_url_works(self):
|
||||
|
||||
# test the api_base_url feature, and that it can contain a path
|
||||
config = AppConfig()
|
||||
backend_port = find_available_port("localhost", 10000)
|
||||
config.update_server_config(
|
||||
app__api_base_url=f"http://localhost:{backend_port}/additional/path",
|
||||
multi_dataset__dataroot=f"{PROJECT_ROOT}/example-dataset",
|
||||
)
|
||||
|
||||
config.complete_config()
|
||||
|
||||
with test_server(["-p", str(backend_port)], app_config=config) as server:
|
||||
session = requests.Session()
|
||||
self.assertEqual(server, f"http://localhost:{backend_port}")
|
||||
response = session.get(f"{server}/additional/path/d/pbmc3k.h5ad/api/v0.2/config")
|
||||
self.assertEqual(response.status_code, 200)
|
||||
data_config = response.json()
|
||||
self.assertEqual(data_config["config"]["displayNames"]["dataset"], "pbmc3k")
|
||||
|
||||
# test the health check at the correct url
|
||||
response = session.get(f"{server}/additional/path/health")
|
||||
assert response.json()["status"] == "pass"
|
||||
|
||||
# also check that the old URL still works.
|
||||
# NOTE: this old URL location will soon be deprecated, and when that happens
|
||||
# this check can be removed.
|
||||
response = session.get(f"{server}/health")
|
||||
assert response.json()["status"] == "pass"
|
||||
|
||||
def test_get_web_base_url_works(self):
|
||||
config = self.get_config(web_base_url="www.thisisawebsite.com")
|
||||
web_base_url = config.server_config.get_web_base_url()
|
||||
self.assertEqual(web_base_url, "www.thisisawebsite.com")
|
||||
|
||||
config = self.get_config(web_base_url="local", port=12)
|
||||
web_base_url = config.server_config.get_web_base_url()
|
||||
self.assertEqual(web_base_url, "http://localhost:12")
|
||||
|
||||
config = self.get_config(web_base_url="www.thisisawebsite.com/")
|
||||
web_base_url = config.server_config.get_web_base_url()
|
||||
self.assertEqual(web_base_url, "www.thisisawebsite.com")
|
||||
|
||||
config = self.get_config(api_base_url="www.api_base.com/")
|
||||
web_base_url = config.server_config.get_web_base_url()
|
||||
self.assertEqual(web_base_url, "www.api_base.com")
|
||||
|
||||
def test_config_for_single_dataset(self):
|
||||
file_name = self.custom_app_config(
|
||||
config_file_name="single_dataset.yml", dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k.cxg"
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
config.server_config.handle_single_dataset(self.context)
|
||||
self.assertIsNotNone(config.server_config.matrix_data_cache_manager)
|
||||
|
||||
file_name = self.custom_app_config(
|
||||
config_file_name="single_dataset_with_about.yml",
|
||||
about="www.cziscience.com",
|
||||
dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k.cxg",
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(file_name)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
config.server_config.handle_single_dataset(self.context)
|
||||
|
||||
def test_multi_dataset_raises_error_for_illegal_routes(self):
|
||||
# test for illegal url_dataroots
|
||||
for illegal in ("../b", "!$*", "\\n", "", "(bad)"):
|
||||
self.config.update_server_config(
|
||||
multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
|
||||
)
|
||||
with self.assertRaises(ConfigurationError):
|
||||
self.config.complete_config()
|
||||
|
||||
def test_multidataset_works_for_legal_routes(self):
|
||||
# test for legal url_dataroots
|
||||
for legal in ("d", "this.is-okay_", "a/b"):
|
||||
self.config.update_server_config(
|
||||
multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
|
||||
)
|
||||
self.config.complete_config()
|
||||
|
||||
def test_mulitdatasets_work_e2e(self):
|
||||
# test that multi dataroots work end to end
|
||||
self.config.update_server_config(
|
||||
multi_dataset__dataroot=dict(
|
||||
s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"),
|
||||
s2=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set2"),
|
||||
s3=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set3"),
|
||||
)
|
||||
)
|
||||
|
||||
# Change this default to test if the dataroot overrides below work.
|
||||
self.config.update_default_dataset_config(app__about_legal_tos="tos_default.html")
|
||||
|
||||
# specialize the configs for set1
|
||||
self.config.add_dataroot_config(
|
||||
"s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html"
|
||||
)
|
||||
|
||||
# specialize the configs for set2
|
||||
self.config.add_dataroot_config(
|
||||
"s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html"
|
||||
)
|
||||
|
||||
# no specializations for set3 (they get the default dataset config)
|
||||
self.config.complete_config()
|
||||
|
||||
with test_server(app_config=self.config) as server:
|
||||
session = requests.Session()
|
||||
|
||||
response = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config")
|
||||
data_config = response.json()
|
||||
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
|
||||
assert data_config["config"]["parameters"]["annotations"] is False
|
||||
assert data_config["config"]["parameters"]["disable-diffexp"] is False
|
||||
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html"
|
||||
|
||||
response = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config")
|
||||
data_config = response.json()
|
||||
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
|
||||
assert data_config["config"]["parameters"]["annotations"] is True
|
||||
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html"
|
||||
|
||||
response = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config")
|
||||
data_config = response.json()
|
||||
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
|
||||
assert data_config["config"]["parameters"]["annotations"] is True
|
||||
assert data_config["config"]["parameters"]["disable-diffexp"] is False
|
||||
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html"
|
||||
|
||||
response = session.get(f"{server}/health")
|
||||
assert response.json()["status"] == "pass"
|
||||
|
||||
@patch("server.common.config.server_config.diffexp_tiledb.set_config")
|
||||
def test_handle_diffexp(self, mock_tiledb_config):
|
||||
custom_config_file = self.custom_app_config(
|
||||
dataroot=f"{FIXTURES_ROOT}",
|
||||
cpu_multiplier=3,
|
||||
diffexp_max_workers=1,
|
||||
target_workunit=4,
|
||||
config_file_name=self.config_file_name,
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(custom_config_file)
|
||||
config.server_config.handle_diffexp()
|
||||
# called with the min of diffexp_max_workers and cpus*cpu_multiplier
|
||||
mock_tiledb_config.assert_called_once_with(1, 4)
|
||||
|
||||
@patch("server.data_cxg.cxg_adaptor.CxgAdaptor.set_tiledb_context")
|
||||
def test_handle_adaptor(self, mock_tiledb_context):
|
||||
custom_config = self.custom_app_config(
|
||||
dataroot=f"{FIXTURES_ROOT}", cxg_tile_cache_size=10, cxg_num_reader_threads=2
|
||||
)
|
||||
config = AppConfig()
|
||||
config.update_from_config_file(custom_config)
|
||||
config.server_config.handle_adaptor()
|
||||
mock_tiledb_context.assert_called_once_with(
|
||||
{"sm.tile_cache_size": 10, "sm.num_reader_threads": 2, "vfs.s3.region": "us-east-1"}
|
||||
)
|
||||
|
||||
@mockenv(CXG_AWS_SECRET_NAME="TESTING", CXG_AWS_SECRET_REGION_NAME="TEST_REGION")
|
||||
@patch("server.common.config.get_secret_key")
|
||||
def test_get_config_vars_from_aws_secrets(self, mock_get_secret_key):
|
||||
mock_get_secret_key.return_value = {
|
||||
"flask_secret_key": "mock_flask_secret",
|
||||
"oauth_client_secret": "mock_oauth_secret",
|
||||
"db_uri": "mock_db_uri",
|
||||
}
|
||||
|
||||
config = AppConfig()
|
||||
|
||||
with self.assertLogs(level="INFO") as logger:
|
||||
from server.common.config import handle_config_from_secret
|
||||
|
||||
# should not throw error
|
||||
# "AttributeError: 'XConfig' object has no attribute 'x'"
|
||||
handle_config_from_secret(config)
|
||||
|
||||
# should log 3 lines (one for each var set from a secret)
|
||||
self.assertEqual(len(logger.output), 3)
|
||||
self.assertIn("INFO:root:set app__flask_secret_key from secret", logger.output[0])
|
||||
self.assertIn("INFO:root:set authentication__params_oauth__client_secret from secret", logger.output[1])
|
||||
self.assertIn("INFO:root:set user_annotations__hosted_tiledb_array__db_uri from secret", logger.output[2])
|
||||
self.assertEqual(config.server_config.app__flask_secret_key, "mock_flask_secret")
|
||||
self.assertEqual(config.server_config.authentication__params_oauth__client_secret, "mock_oauth_secret")
|
||||
self.assertEqual(config.default_dataset_config.user_annotations__hosted_tiledb_array__db_uri, "mock_db_uri")
|
||||
Reference in New Issue
Block a user