mirror of
https://github.com/chanzuckerberg/cellxgene.git
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e4bf65c54a
* Improve hosted cellxgene - option to turn off the test index page, or supply a page for redirect. For EB, The default is to return 404. For cli launch, the default is the test page. - option to select which matrix types are allowed for multi dataset servers. For EB, The default is CXG only. For cli launch, the default is any matrix type. - Return early with an error response if diffexp is requested when not configured - Verified that reembedings and user annotations also return with an error response if used when not enabled. TODO: The new options cannot currently be set by the user. I plan to add a configuration file where these and all other settings can be set. Fixes #1210 Fixes #1228 Fixes #1229
73 lines
2.0 KiB
Python
73 lines
2.0 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=True,
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multi_dataset_index=None,
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multi_dataset_allowed_matrix_type=["cxg"],
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)
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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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