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b3e9719602
* early, non-working eb config * hosted cellxgene In this PR, contains scripts and instructions for deploying cellxgene for AWS elastic beanstalk. It supports the multi-dataset option. The Makefile in the server/eb directory creates an artifact.zip file, which can be deploy at AWS EB. The server/eb directory contains: app.py - flask app to run the server Makefile - which creates an artifact.zip file which can be deployed. README.md - instructions for setting up and deploying the eb app. * hosted cellxgene (#38) In this PR, contains scripts and instructions for deploying cellxgene for AWS elastic beanstalk. It supports the multi-dataset option. The Makefile in the server/eb directory creates an artifact.zip file, which can be deploy at AWS EB. The server/eb directory contains: app.py - flask app to run the server Makefile - which creates an artifact.zip file which can be deployed. README.md - instructions for setting up and deploying the eb app. * Update how artifact.zip is created prune the server/test and server/eb directories * Remove debugging print statements * fixes from review comments * fix lint Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
70 lines
1.9 KiB
Python
70 lines
1.9 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.exception("Exception importing server modules")
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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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if dataroot is None:
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logging.error("CXG_DATAROOT environment variable must be set")
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sys.exit(1)
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app_config = AppConfig(
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datapath=None,
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dataroot=dataroot,
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title="",
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about=None,
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scripts=[],
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layout=[],
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max_category_items=100,
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diffexp_lfc_cutoff=0.01,
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obs_names=None,
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var_names=None,
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anndata_backed=False,
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disable_diffexp=False)
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matrix_data_cache_manager = MatrixDataCacheManager()
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annotations = None
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server = Server(matrix_data_cache_manager, 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.exception("Caught exception during initialization")
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sys.exit(1)
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logging.info(f"starting server with CXG_DATAROOT={dataroot}")
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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.exception("Caught exception during server run")
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sys.exit(1)
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