mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-25 05:18:11 +08:00
80 lines
2.4 KiB
Python
80 lines
2.4 KiB
Python
import os
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import argparse
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from flask import Flask
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from flask_compress import Compress
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from flask_cors import CORS
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from flask_restful_swagger_2 import get_swagger_blueprint
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from .web import webapp
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from .rest_api.rest import get_api_resources
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REACTIVE_LIMIT = 1_000_000
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app = Flask(__name__)
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Compress(app)
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CORS(app)
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# Config
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CXG_DIR = os.environ.get("CXG_DIRECTORY", default="example-dataset/")
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SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
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ENGINE = os.environ.get("CXG_ENGINE", default="scanpy")
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TITLE = os.environ.get("DATASET_TITLE", default="PBMC 3K")
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# TODO remove the 2 when this is prod
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CXG_API_BASE = os.environ.get("CXG_API_BASE2", default="http://0.0.0.0:5005/api/")
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app.config.update(
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SECRET_KEY=SECRET_KEY,
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CXG_API_BASE=CXG_API_BASE,
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ENGINE=ENGINE,
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DATA=CXG_DIR,
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DATASET_TITLE=TITLE
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)
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app.config["PROFILE"] = True
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# app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[15])
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# Application Data
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data = None
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# A list of swagger document objects
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docs = []
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resources = get_api_resources()
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docs.append(resources.get_swagger_doc())
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app.register_blueprint(webapp.bp)
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app.register_blueprint(resources.blueprint)
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app.register_blueprint(
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get_swagger_blueprint(docs, "/api/swagger", produces=["application/json"], title="cellxgene rest api",
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description="An API connecting ExpressionMatrix2 clustering algorithm to cellxgene"))
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app.add_url_rule("/", endpoint="index")
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def run(args):
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global data
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app.config.update(
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ENGINE=args.engine,
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DATA=args.data_directory
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)
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if app.config["ENGINE"] == "scanpy":
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from .scanpy_engine.scanpy_engine import ScanpyEngine
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data = ScanpyEngine(app.config["DATA"], schema="data_schema.json")
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app.run(host="0.0.0.0", debug=True, port=5005)
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def main():
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parser = argparse.ArgumentParser(description="AAAAA")
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subparsers = parser.add_subparsers(dest="cellxgene_command")
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run_subparser = subparsers.add_parser('run', help="run cellxgene")
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run_subparser.add_argument('engine', metavar='engine', help='Format that the backend uses for data')
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run_subparser.add_argument('data_directory', metavar='dir',
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help='Directory containing data and schema')
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run_subparser.set_defaults(func=run)
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args = parser.parse_args()
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args.func(args)
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# app.run(host="0.0.0.0", debug=True, port=5005)
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