mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 22:08:00 +08:00
89 lines
2.9 KiB
Python
89 lines
2.9 KiB
Python
import argparse
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import os
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import warnings
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from flask import Flask
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from flask_caching import Cache
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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 .rest_api.rest import get_api_resources
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from .util.utils import Float32JSONEncoder
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from .web import webapp
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REACTIVE_LIMIT = 1_000_000
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app = Flask(__name__, static_folder="web/static")
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app.json_encoder = Float32JSONEncoder
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cache = Cache(app, config={"CACHE_TYPE": "simple", "CACHE_DEFAULT_TIMEOUT": 860000})
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Compress(app)
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CORS(app)
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# Config
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SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
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app.config.update(
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SECRET_KEY=SECRET_KEY,
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)
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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_scanpy(args):
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title = args.title
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if not title:
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title = os.path.basename(os.path.normpath(args.data_directory))
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api_base = f"http://127.0.0.1:{args.port}/api/"
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app.config.update(
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DATASET_TITLE=title,
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CXG_API_BASE=api_base
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)
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from .scanpy_engine.scanpy_engine import ScanpyEngine
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app.data = ScanpyEngine(args.data_directory, layout_method=args.layout, diffexp_method=args.diffexp)
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if args.bind_all:
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host = "0.0.0.0"
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else:
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host = "127.0.0.1"
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app.run(host=host, debug=True, port=args.port)
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def main():
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parser = argparse.ArgumentParser(description="Cellxgene is a tool for exploring single cell expression.")
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parser.add_argument("--title", "-t", help="Title to display -- if this is omitted the title will be the name "
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"of the directory from the data_directory arg")
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parser.add_argument("--port", help="Port to run server on.", type=int, default=5005)
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parser.add_argument(
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"--bind-all",
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help="Bind to all interfaces (this makes the server accessible beyond this computer)",
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action="store_true")
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subparsers = parser.add_subparsers(dest="engine")
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subparsers.required = True
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try:
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from .scanpy_engine.scanpy_engine import ScanpyEngine
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except ImportError:
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warnings.simplefilter('default', ImportWarning) # Enable ImportWarning
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warnings.warn("Scanpy engine not available", ImportWarning)
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else:
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ScanpyEngine.add_to_parser(subparsers, run_scanpy)
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if len(subparsers.choices) == 0:
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raise ImportError('Could not import any engines, see warnings above')
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args = parser.parse_args()
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args.func(args)
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