mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 22:08:00 +08:00
62 lines
1.9 KiB
Python
62 lines
1.9 KiB
Python
import os
|
|
|
|
from flask import Flask
|
|
from flask_compress import Compress
|
|
from flask_cors import CORS
|
|
from flask_restful_swagger_2 import get_swagger_blueprint
|
|
|
|
from .web import webapp
|
|
from .rest_api.rest import get_api_resources
|
|
|
|
app = Flask(__name__)
|
|
Compress(app)
|
|
CORS(app)
|
|
|
|
# Config
|
|
CONFIG_FILE = os.environ.get("CXG_CONFIG_FILE", default="scanpy-test.cfg")
|
|
CXG_DIR = os.environ.get("CXG_DIRECTORY", default="/Users/charlotteweaver/Documents/Git/cxg-v2/data/")
|
|
SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
|
|
ENGINE = os.environ.get("CXG_ENGINE", default="scanpy")
|
|
TITLE = os.environ.get("DATASET_TITLE", default="PBMC 3K")
|
|
# TODO remove the 2 when this is prod
|
|
CXG_API_BASE = os.environ.get("CXG_API_BASE2", default="http://0.0.0.0:5005/api/")
|
|
|
|
if not CONFIG_FILE:
|
|
raise ValueError("No config file set for Flask application")
|
|
|
|
# TODO check what is actually being configured here
|
|
app.config.from_pyfile(os.path.join(CXG_DIR, "config", CONFIG_FILE), silent=True)
|
|
app.config.update(
|
|
SECRET_KEY=SECRET_KEY,
|
|
CXG_API_BASE=CXG_API_BASE,
|
|
ENGINE=ENGINE,
|
|
DATA=CXG_DIR,
|
|
DATASET_TITLE=TITLE
|
|
)
|
|
|
|
app.config['PROFILE'] = True
|
|
# app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[15])
|
|
|
|
# Application Data
|
|
data = None
|
|
if app.config["ENGINE"] == "scanpy":
|
|
from .scanpy_engine.scanpy_engine import ScanpyEngine
|
|
data = ScanpyEngine(app.config["DATA"], schema="data_schema.json")
|
|
|
|
REACTIVE_LIMIT = 1_000_000
|
|
|
|
# A list of swagger document objects
|
|
docs = []
|
|
resources = get_api_resources()
|
|
docs.append(resources.get_swagger_doc())
|
|
|
|
|
|
app.register_blueprint(webapp.bp)
|
|
app.register_blueprint(resources.blueprint)
|
|
app.register_blueprint(
|
|
get_swagger_blueprint(docs, '/api/swagger', produces=["application/json"], title="cellxgene rest api",
|
|
description='An API connecting ExpressionMatrix2 clustering algorithm to cellxgene'))
|
|
|
|
|
|
app.add_url_rule('/', endpoint='index')
|