Add backend to cellxgene repo

backend/app/__init__.py

@@ -0,0 +1,63 @@
+import os
+
+from flask import Flask, url_for, g
+from flask_compress import Compress
+from flask_cors import CORS
+from flask_restful_swagger_2 import get_swagger_blueprint
+
+# from werkzeug.contrib.profiler import ProfilerMiddleware
+
+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/")
+SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
+# 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")
+
+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,
+)
+app.config.update(
+    DATA=os.path.join(CXG_DIR, app.config["DATA_DIR"]),
+)
+
+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"])
+
+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')
+
+
+if __name__ == "__main__":
+    app.run(host='0.0.0.0', debug=True, port=5005)