mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-03 10:08:12 +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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