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Added cli command for run

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Charlotte Weaver
2018-07-19 17:21:28 -07:00
parent 45f61d87d7
commit 2c7a11ab80
1 changed files with 16 additions and 23 deletions
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server/app/app.py
+16 -23
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@@ -16,24 +16,12 @@ Compress(app)
CORS(app) CORS(app)
# Config # Config
CXG_DIR = os.environ.get("CXG_DIRECTORY", default="example-dataset/")
SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine") 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( app.config.update(
SECRET_KEY=SECRET_KEY, 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 # Application Data
data = None data = None
@@ -54,26 +42,31 @@ app.add_url_rule("/", endpoint="index")
def run(args): def run(args):
global data global data
title = args.title
if not title:
title = os.path.basename(os.path.normpath(args.data_directory))
api_base = f"http://0.0.0.0:{args.port}/api/"
app.config.update( app.config.update(
ENGINE=args.engine, DATASET_TITLE=title,
DATA=args.data_directory CXG_API_BASE=api_base
) )
if app.config["ENGINE"] == "scanpy": if args.engine == "scanpy":
from .scanpy_engine.scanpy_engine import ScanpyEngine from .scanpy_engine.scanpy_engine import ScanpyEngine
data = ScanpyEngine(app.config["DATA"], schema="data_schema.json") data = ScanpyEngine(args.data_directory, schema="data_schema.json")
app.run(host="0.0.0.0", debug=True, port=args.port)
app.run(host="0.0.0.0", debug=True, port=5005)
def main(): def main():
parser = argparse.ArgumentParser(description="AAAAA") parser = argparse.ArgumentParser(description="Cellxgene is a tool for exploring single cell expression.")
subparsers = parser.add_subparsers(dest="cellxgene_command") subparsers = parser.add_subparsers(dest="cellxgene_command")
run_subparser = subparsers.add_parser('run', help="run cellxgene") run_subparser = subparsers.add_parser("run", help="run cellxgene")
run_subparser.add_argument('engine', metavar='engine', help='Format that the backend uses for data') run_subparser.add_argument("--title", "-t", help="Title to display (default = data directory name")
run_subparser.add_argument('data_directory', metavar='dir', run_subparser.add_argument("--port", help="Port to run server on.", type=int, default=5005)
help='Directory containing data and schema') run_subparser.add_argument("engine", help="The underlying structure of the data")
run_subparser.add_argument("data_directory", metavar="dir", help="Directory containing data and schema")
run_subparser.set_defaults(func=run) run_subparser.set_defaults(func=run)
args = parser.parse_args() args = parser.parse_args()
args.func(args) args.func(args)
# app.run(host="0.0.0.0", debug=True, port=5005) # app.run(host="0.0.0.0", debug=True, port=5005)