mirror of
https://github.com/chanzuckerberg/cellxgene.git
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d99b84ba09
* work around anndata bug 344 * fix accidental cut and paste error * Use modified make_index_unique function Temporarily copy code from https://github.com/theislab/anndata/pull/345 until the issue is resolved and released. * Add notes and test for make_index_unique * Lint fix * Format python Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
75 lines
2.5 KiB
Python
75 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(multi_dataset__dataroot=dataroot,)
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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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