Merge pull request #116 from chanzuckerberg/csweaver/packaging

Csweaver/packaging

.gitignore

@@ -44,3 +44,9 @@ server/app/web/static/css/
 server/app/web/static/img/
 server/app/web/static/js/
 server/app/web/templates/index\.html
+
+
+*.egg-info
+dist/*
+build/*
+

MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include server/app/web/templates *
+recursive-include server/app/web/static *

bin/build-client

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+npm install --prefix client/ client
+npm run  --prefix client build
+mkdir -p server/app/web/static/img
+cp client/build/index.html server/app/web/templates/
+cp -r client/build/static server/app/web/
+
+cp client/build/favicon.png server/app/web/static/img
+cp client/build/service-worker.js server/app/web/static/js/

example-dataset/data_schema.json

@@ -0,0 +1,32 @@
+{
+	"CellName": {
+		"type": "string",
+		"variabletype": "categorical",
+		"displayname": "Name",
+		"include": true
+	},
+	"n_genes": {
+		"type": "int",
+		"variabletype": "continuous",
+		"displayname": "Num Genes",
+		"include": true
+	},
+	"percent_mito": {
+		"type": "float",
+		"variabletype": "continuous",
+		"displayname": "Mitochondrial Percentage",
+		"include": true
+	},
+	"n_counts": {
+		"type": "float",
+		"variabletype": "continuous",
+		"displayname": "Num Counts",
+		"include": true
+	},
+    "louvain": {
+		"type": "string",
+		"variabletype": "categorical",
+		"displayname": "Louvain Cluster",
+		"include": true
+	}
+}

server/app/__init__.py

@@ -1,55 +0,0 @@
-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")

server/app/app.py

@@ -0,0 +1,57 @@
+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 app import data, REACTIVE_LIMIT
+        from server.app.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 app import data
+        from server.app.app import data
         payload = {
             "metadata": [],
             "cellcount": 0,
@@ -199,8 +199,8 @@ class CellsAPI(Resource):
             "ranges": {},
         }
         # get query params
-        filter = parse_filter(request.args, data.schema)
+        cells_filter = parse_filter(request.args, data.schema)
-        filtered_data = data.filter_cells(filter)
+        filtered_data = data.filter_cells(cells_filter)
         payload["metadata"] = data.metadata(filtered_data)
         payload["ranges"] = data.metadata_ranges(filtered_data)
         payload["graph"] = data.create_graph(filtered_data)
@@ -251,7 +251,7 @@ class ExpressionAPI(Resource):
         }
     })
     def get(self):
-        from app import data
+        from server.app.app import data
         expression_data = data.expression()
         return make_payload(expression_data)
 
@@ -309,7 +309,7 @@ class ExpressionAPI(Resource):
         }
     })
     def post(self):
-        from app import data
+        from server.app.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 app import data
+        from server.app.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
@@ -38,4 +38,4 @@ six==1.11.0
 statsmodels==0.9.0
 tables==3.4.4
 urllib3==1.23
-Werkzeug==0.14.1
+Werkzeug==0.14.1

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

@@ -0,0 +1,30 @@
+from setuptools import setup, find_packages
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+with open('server/requirements.txt') as fh:
+    requirements = fh.read().splitlines()
+
+setup(
+    name='cellxgene',
+    version='0.0.1',
+    packages=find_packages(),
+    url='https://github.com/chanzuckerberg/cellxgene',
+    license='MIT',
+    author='Colin Megill, Charlotte Weaver',
+    author_email='cweaver@chanzuckerberg.com',
+    description='Web application for exploration of large scale scRNA-seq datasets',
+    long_description=long_description,
+    install_requires=requirements,
+    include_package_data=True,
+    zip_safe=False,
+    classifiers=(
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+    ),
+    entry_points={
+        'console_scripts':
+            ['cellxgene = server.app.app:main']
+    }
+)