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Address PR review issues

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Charlotte Weaver
2018-07-20 11:43:31 -07:00
parent 9c72f2c2d5
commit de5e0f4ea7
1 changed files with 11 additions and 14 deletions
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server/app/app.py
+11 -14
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@@ -1,5 +1,5 @@
import os
import argparse import argparse
import os
from flask import Flask from flask import Flask
from flask_compress import Compress from flask_compress import Compress
@@ -40,7 +40,7 @@ app.register_blueprint(
app.add_url_rule("/", endpoint="index") app.add_url_rule("/", endpoint="index")
def run(args): def run_scanpy(args):
global data global data
title = args.title title = args.title
if not title: if not title:
@@ -50,23 +50,20 @@ def run(args):
DATASET_TITLE=title, DATASET_TITLE=title,
CXG_API_BASE=api_base CXG_API_BASE=api_base
) )
if args.engine == "scanpy":
from .scanpy_engine.scanpy_engine import ScanpyEngine from .scanpy_engine.scanpy_engine import ScanpyEngine
data = ScanpyEngine(args.data_directory, 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=args.port)
def main(): def main():
parser = argparse.ArgumentParser(description="Cellxgene is a tool for exploring single cell expression.") parser = argparse.ArgumentParser(description="Cellxgene is a tool for exploring single cell expression.")
parser.add_argument("--title", "-t", help="Title to display -- if this is omitted the title will be the name "
"of the directory from the data_directory arg")
parser.add_argument("--port", help="Port to run server on.", type=int, default=5005)
subparsers = parser.add_subparsers(dest="cellxgene_command") subparsers = parser.add_subparsers(dest="cellxgene_command")
run_subparser = subparsers.add_parser("run", help="run cellxgene") scanpy_subparser = subparsers.add_parser("scanpy", help="run cellxgene using the scanpy engine")
run_subparser.add_argument("--title", "-t", help="Title to display (default = data directory name") scanpy_subparser.add_argument("data_directory", metavar="dir", help="Directory containing data and schema file")
run_subparser.add_argument("--port", help="Port to run server on.", type=int, default=5005) scanpy_subparser.set_defaults(func=run_scanpy)
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)
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)