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Move data to a property of the app object

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This commit is contained in:
Charlotte Weaver
2018-08-02 16:18:17 -07:00
parent 64bfb7416e
commit 8dbb131afd
2 changed files with 19 additions and 20 deletions
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server/app/app.py
+1 -2
View File
@@ -43,7 +43,6 @@ app.add_url_rule("/", endpoint="index")
def run_scanpy(args): def run_scanpy(args):
global data
title = args.title title = args.title
if not title: if not title:
title = os.path.basename(os.path.normpath(args.data_directory)) title = os.path.basename(os.path.normpath(args.data_directory))
@@ -54,7 +53,7 @@ def run_scanpy(args):
) )
from .scanpy_engine.scanpy_engine import ScanpyEngine from .scanpy_engine.scanpy_engine import ScanpyEngine
data = ScanpyEngine(args.data_directory, schema="data_schema.json") app.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)
server/app/rest_api/rest.py
+18 -18
View File
@@ -88,13 +88,13 @@ class InitializeAPI(Resource):
} }
}) })
def get(self): def get(self):
from server.app.app import data, REACTIVE_LIMIT from server.app.app import app, REACTIVE_LIMIT
return make_payload({ return make_payload({
"schema": data.schema, "schema": app.data.schema,
"cellcount": data.cell_count, "cellcount": app.data.cell_count,
"reactivelimit": REACTIVE_LIMIT, "reactivelimit": REACTIVE_LIMIT,
"genes": data.genes(), "genes": app.data.genes(),
"ranges": data.metadata_ranges(), "ranges": app.data.metadata_ranges(),
}) })
@@ -191,7 +191,7 @@ class CellsAPI(Resource):
} }
}) })
def get(self): def get(self):
from server.app.app import data from server.app.app import app
payload = { payload = {
"metadata": [], "metadata": [],
"cellcount": 0, "cellcount": 0,
@@ -199,12 +199,12 @@ class CellsAPI(Resource):
"ranges": {}, "ranges": {},
} }
# get query params # get query params
cells_filter = parse_filter(request.args, data.schema) cells_filter = parse_filter(request.args, app.data.schema)
filtered_data = data.filter_cells(cells_filter) filtered_data = app.data.filter_cells(cells_filter)
payload["metadata"] = data.metadata(filtered_data) payload["metadata"] = app.data.metadata(filtered_data)
payload["ranges"] = data.metadata_ranges(filtered_data) payload["ranges"] = app.data.metadata_ranges(filtered_data)
payload["graph"] = data.create_graph(filtered_data) payload["graph"] = app.data.create_graph(filtered_data)
payload["cellcount"] = data.cell_count payload["cellcount"] = app.data.cell_count
return make_payload(payload) return make_payload(payload)
@@ -251,8 +251,8 @@ class ExpressionAPI(Resource):
} }
}) })
def get(self): def get(self):
from server.app.app import data from server.app.app import app
expression_data = data.expression() expression_data = app.data.expression()
return make_payload(expression_data) return make_payload(expression_data)
@swagger.doc({ @swagger.doc({
@@ -309,14 +309,14 @@ class ExpressionAPI(Resource):
} }
}) })
def post(self): def post(self):
from server.app.app import data from server.app.app import app
args = request.get_json() args = request.get_json()
cell_list = args.get("celllist", []) cell_list = args.get("celllist", [])
gene_list = args.get("genelist", []) gene_list = args.get("genelist", [])
if not cell_list and not gene_list: if not cell_list and not gene_list:
return make_payload([], "must include celllist and/or genelist parameter", 400) return make_payload([], "must include celllist and/or genelist parameter", 400)
expression_data = data.expression(cell_list, gene_list) expression_data = app.data.expression(cell_list, gene_list)
if cell_list and len(expression_data["cells"]) < len(cell_list): if cell_list and len(expression_data["cells"]) < len(cell_list):
return make_payload([], "Some cell ids not available", 400) return make_payload([], "Some cell ids not available", 400)
@@ -415,7 +415,7 @@ class DifferentialExpressionAPI(Resource):
} }
}) })
def post(self): def post(self):
from server.app.app import data from server.app.app import app
args = request.get_json() args = request.get_json()
cell_list_1 = args.get("celllist1", []) cell_list_1 = args.get("celllist1", [])
cell_list_2 = args.get("celllist2", []) cell_list_2 = args.get("celllist2", [])
@@ -425,7 +425,7 @@ class DifferentialExpressionAPI(Resource):
return make_payload([], return make_payload([],
"must include celllist1 and celllist2 parameters", "must include celllist1 and celllist2 parameters",
400) 400)
data = data.diffexp(cell_list_1, cell_list_2, pval, num_genes) data = app.data.diffexp(cell_list_1, cell_list_2, pval, num_genes)
return make_payload(data) return make_payload(data)