Added entry point to run cellxgene from console

server/app/__init__.py

@@ -1,55 +1 @@
-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
-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/")
-
-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")
+from . import app

server/app/app.py

@@ -0,0 +1,62 @@
+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
+
+REACTIVE_LIMIT = 1_000_000
+
+
+app = Flask(__name__)
+Compress(app)
+CORS(app)
+
+# Config
+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/")
+
+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")
+
+
+
+# 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")
+
+
+def main():
+    app.run(host="0.0.0.0", debug=True, port=5005)
+

server/app/rest_api/rest.py

@@ -88,7 +88,7 @@ class InitializeAPI(Resource):
         }
     })
     def get(self):
-        from .. import data, REACTIVE_LIMIT
+        from ..app import data, REACTIVE_LIMIT
         return make_payload({
             "schema": data.schema,
             "cellcount": data.cell_count,
@@ -191,7 +191,7 @@ class CellsAPI(Resource):
         }
     })
     def get(self):
-        from .. import data
+        from ..app import data
         payload = {
             "metadata": [],
             "cellcount": 0,
@@ -251,7 +251,7 @@ class ExpressionAPI(Resource):
         }
     })
     def get(self):
-        from .. import data
+        from ..app import data
         expression_data = data.expression()
         return make_payload(expression_data)
 
@@ -309,7 +309,7 @@ class ExpressionAPI(Resource):
         }
     })
     def post(self):
-        from .. import data
+        from ..app import data
         args = request.get_json()
         cell_list = args.get("celllist", [])
         gene_list = args.get("genelist", [])
@@ -415,7 +415,7 @@ class DifferentialExpressionAPI(Resource):
         }
     })
     def post(self):
-        from .. import data
+        from ..app import data
         args = request.get_json()
         cell_list_1 = args.get("celllist1", [])
         cell_list_2 = args.get("celllist2", [])

server/requirements.txt

@@ -1,5 +1,5 @@
 aniso8601==3.0.2
-anndata==0.6.1
+anndata==0.6.4
 certifi==2018.4.16
 chardet==3.0.4
 click==6.7
@@ -30,7 +30,7 @@ pyparsing==2.2.0
 python-dateutil==2.7.3
 pytz==2018.4
 requests==2.19.1
-scanpy==1.2.2
+scanpy==1.0.4
 scikit-learn==0.19.1
 scipy==1.1.0
 seaborn==0.8.1

server/run.py

@@ -1,3 +1,3 @@
-from app import app
+from app.app import app
 
 app.run(host="0.0.0.0", debug=True, port=5005)

setup.py

@@ -16,7 +16,6 @@ setup(
     author_email='cweaver@chanzuckerberg.com',
     description='Web application for exploration of large scale scRNA-seq datasets',
     long_description=long_description,
-    long_description_content_type="text/markdown",
     install_requires=requirements,
     include_package_data=True,
     zip_safe=False,
@@ -24,4 +23,8 @@ setup(
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
     ),
+    entry_points={
+        'console_scripts':
+            ['cellxgene = server.app.app:main']
+    }
 )