mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-21 06:18:12 +08:00
bmccandless
8180be83b8
* Introduce a config file to cellxgene The config file format is in yaml. The default config is located in server/common/default_config.py. A user may create a yaml file that contains a subset of these fields. It can be used during cellxgene launch, or for hosted cellxgene. The code has also been refactored. Much of the logic to check arguments has moved from launch to app config. It is now possible to set the tiledb context parameters using the config file. Other feature will soon be handled in a similar way.
77 lines
2.5 KiB
Python
77 lines
2.5 KiB
Python
"""cellxgene AWS elastic beanstalk application"""
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import sys
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import os
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import logging
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if os.path.isdir("/opt/python/log"):
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# This is the standard location where Amazon EC2 instances store the application logs.
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logging.basicConfig(
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filename="/opt/python/log/app.log",
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level=logging.DEBUG,
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format="%(asctime)s.%(msecs)03d %(levelname)s %(module)s - %(funcName)s: %(message)s",
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datefmt="%Y-%m-%d %H:%M:%S",
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)
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# echo the logs to stdout. Useful for local testing
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logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
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SERVERDIR = os.path.dirname(os.path.realpath(__file__))
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sys.path.append(SERVERDIR)
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try:
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from server.common.app_config import AppConfig
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from server.app.app import Server
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from server.data_common.matrix_loader import MatrixDataCacheManager
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except Exception:
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logging.critical("Exception importing server modules", exc_info=True)
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sys.exit(1)
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try:
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dataroot = os.getenv("CXG_DATAROOT")
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app_config = AppConfig()
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config_file = "config.yaml"
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if os.path.exists(config_file):
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logging.info(f"Configuration from {config_file}")
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app_config.update_from_config_file(config_file)
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if dataroot:
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logging.info(f"Configuration from CXG_DATAROOT")
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app_config.update(
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multi_dataset__dataroot=dataroot,
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)
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# features are unsupported in the current hosted server
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app_config.update(
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diffexp__enable=False,
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user_annotations__enable=False,
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embeddings__enable_reembedding=False,
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multi_dataset__allowed_matrix_types=["cxg"],
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)
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matrix_data_cache_manager = MatrixDataCacheManager()
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app_config.complete_config(matrix_data_cache_manager, logging.info)
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user_annotations = app_config.user_annotations
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server = Server(matrix_data_cache_manager, user_annotations, app_config)
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debug = False
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application = server.app
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except Exception:
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logging.critical("Caught exception during initialization", exc_info=True)
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sys.exit(1)
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if app_config.multi_dataset__dataroot:
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logging.info(f"starting server with multi_dataset__dataroot={app_config.multi_dataset__dataroot}")
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elif app_config.single_dataset__datapath:
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logging.info(f"starting server with single_dataset__datapath={app_config.single_dataset__datapath}")
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if __name__ == "__main__":
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try:
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application.run(debug=debug, threaded=not debug, use_debugger=False)
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except Exception:
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logging.critical("Caught exception during initialization", exc_info=True)
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sys.exit(1)
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