mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-01 21:58:12 +08:00
move common code into server, update tests and makefile (#2425)
* move common code into server, update tests and makefile remove backend directory, refactor update smoke tests
This commit is contained in:
Madison Dunitz
@@ -0,0 +1,212 @@
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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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import yaml
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from 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="secret",
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generate_cache_control_headers="false",
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insecure_test_environment="false",
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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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data_locater_region_name="us-east-1",
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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="secret",
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generate_cache_control_headers="false",
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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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data_locater_region_name="us-east-1",
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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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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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local_file_csv_gene_sets_file="null",
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gene_sets_readonly="false",
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embedding_names=[],
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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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environment=None,
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X_approximate_distribution="auto",
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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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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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data_locater_region_name=data_locater_region_name,
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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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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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local_file_csv_gene_sets_file=local_file_csv_gene_sets_file,
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gene_sets_readonly=gene_sets_readonly,
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embedding_names=embedding_names,
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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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X_approximate_distribution=X_approximate_distribution,
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config_file_name=f"temp_dataset_config_{random_num}.yml",
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)
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external_config = self.custom_external_config(
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environment=environment,
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config_file_name=f"temp_external_config_{random_num}.yml",
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)
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with open(configfile, "w") as app_config_file:
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app_config_file.write(open(server_config).read())
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app_config_file.write(open(dataset_config).read())
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app_config_file.write(open(external_config).read())
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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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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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local_file_csv_gene_sets_file="null",
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gene_sets_readonly="false",
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embedding_names=[],
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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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X_approximate_distribution="auto",
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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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def custom_external_config(
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self,
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environment=None,
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config_file_name="external_config.yaml",
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):
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# set to the default if environment is None
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if environment is None:
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environment = [
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dict(name="CXG_SECRET_KEY", path=["server", "app", "flask_secret_key"], required=False),
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]
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external_config = {
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"external": {
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"environment": environment,
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}
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}
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configfile = os.path.join(self.tmp_fixtures_directory, config_file_name)
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with open(configfile, "w") as external_config_file:
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yaml.dump(external_config, external_config_file)
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return configfile
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