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Merge pull request #116 from chanzuckerberg/csweaver/packaging

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Csweaver/packaging
This commit is contained in:
Charlotte Weaver
2018-07-16 11:44:56 -07:00
committed by GitHub
parent 2e1da27a31 02799cea8e
commit 851ddde130
12 changed files with 148 additions and 66 deletions
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.gitignore
+6
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@@ -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
+2
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@@ -0,0 +1,2 @@
recursive-include server/app/web/templates *
recursive-include server/app/web/static *
bin/build-client
Executable
+10
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@@ -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.h5ad
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example-dataset/data_schema.json
+32
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@@ -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/__init__.py
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server/app/__init__.py
-55
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@@ -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
+57
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@@ -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
+7 -7
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@@ -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)
filtered_data = data.filter_cells(filter)
cells_filter = parse_filter(request.args, data.schema)
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
+3 -3
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@@ -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 -1
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@@ -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
+30
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@@ -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']
}
)