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Apply yapf to python files

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This commit is contained in:
Matt Weiden
2019-12-19 15:20:41 -08:00
parent 42a8d45bd7
commit cdca128a01
43 changed files with 1143 additions and 678 deletions
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server/app/rest_api/rest.py
+77 -68
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@@ -8,13 +8,9 @@ from flask_restful import Api, Resource
from server import __version__ as cellxgene_version
from anndata import __version__ as anndata_version
from server.app.util.constants import (
Axis,
DiffExpMode,
JSON_NaN_to_num_warning_msg,
CXGUID,
CXG_ANNO_COLLECTION
)
from server.app.util.constants import (Axis, DiffExpMode,
JSON_NaN_to_num_warning_msg, CXGUID,
CXG_ANNO_COLLECTION)
from server.app.util.errors import (
FilterError,
InteractiveError,
@@ -25,15 +21,20 @@ from server.app.util.errors import (
class SchemaAPI(Resource):
def get(self):
cxguid = get_userid(session)
anno_collection = get_anno_collection(session)
return make_response(
jsonify({"schema": current_app.data.get_schema(uid=cxguid, collection=anno_collection)}), HTTPStatus.OK
)
jsonify({
"schema":
current_app.data.get_schema(uid=cxguid,
collection=anno_collection)
}), HTTPStatus.OK)
class ConfigAPI(Resource):
def get(self):
cxguid = get_userid(session)
anno_collection = get_anno_collection(session)
@@ -69,7 +70,8 @@ class ConfigAPI(Resource):
"about-dataset": current_app.config["ABOUT_DATASET"]
},
"parameters": {
**current_app.data.get_config_parameters(uid=cxguid, collection=anno_collection)
**current_app.data.get_config_parameters(uid=cxguid,
collection=anno_collection)
},
"library_versions": {
"cellxgene": cellxgene_version,
@@ -82,42 +84,48 @@ class ConfigAPI(Resource):
class AnnotationsObsAPI(Resource):
def get(self):
fields = request.args.getlist("annotation-name", None)
preferred_mimetype = request.accept_mimetypes.best_match(
["application/octet-stream"]
)
["application/octet-stream"])
cxguid = get_userid(session)
anno_collection = get_anno_collection(session)
try:
if preferred_mimetype == "application/octet-stream":
fbs = current_app.data.annotation_to_fbs_matrix("obs", fields, uid=cxguid, collection=anno_collection)
return make_response(fbs,
HTTPStatus.OK,
{"Content-Type": "application/octet-stream"})
fbs = current_app.data.annotation_to_fbs_matrix(
"obs", fields, uid=cxguid, collection=anno_collection)
return make_response(
fbs, HTTPStatus.OK,
{"Content-Type": "application/octet-stream"})
else:
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
return make_response(
f"Unsupported MIME type '{request.accept_mimetypes}'",
HTTPStatus.NOT_ACCEPTABLE)
except KeyError:
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
return make_response(f"Error bad key in {fields}",
HTTPStatus.BAD_REQUEST)
except ValueError as e:
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
def put(self):
cxguid = get_userid(session)
anno_collection = request.args.get("annotation-collection-name", default=None)
anno_collection = request.args.get("annotation-collection-name",
default=None)
if anno_collection is not None:
if not is_safe_collection_name(anno_collection):
return make_response(f"Error, bad annotation collection name", HTTPStatus.BAD_REQUEST)
return make_response(f"Error, bad annotation collection name",
HTTPStatus.BAD_REQUEST)
set_anno_collection(session, anno_collection)
else:
anno_collection = get_anno_collection(session)
try:
fbs = request.get_data()
res = current_app.data.annotation_put_fbs("obs", fbs, uid=cxguid, collection=anno_collection)
return make_response(
res, HTTPStatus.OK, {"Content-Type": "application/json"}
)
res = current_app.data.annotation_put_fbs(
"obs", fbs, uid=cxguid, collection=anno_collection)
return make_response(res, HTTPStatus.OK,
{"Content-Type": "application/json"})
except (ValueError, DisabledFeatureError, KeyError) as e:
return make_response(str(e), HTTPStatus.BAD_REQUEST)
except Exception as e:
@@ -125,41 +133,44 @@ class AnnotationsObsAPI(Resource):
class AnnotationsVarAPI(Resource):
def get(self):
fields = request.args.getlist("annotation-name", None)
preferred_mimetype = request.accept_mimetypes.best_match(
["application/octet-stream"]
)
["application/octet-stream"])
try:
if preferred_mimetype == "application/octet-stream":
return make_response(current_app.data.annotation_to_fbs_matrix("var", fields),
HTTPStatus.OK,
{"Content-Type": "application/octet-stream"})
return make_response(
current_app.data.annotation_to_fbs_matrix("var", fields),
HTTPStatus.OK, {"Content-Type": "application/octet-stream"})
else:
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
return make_response(
f"Unsupported MIME type '{request.accept_mimetypes}'",
HTTPStatus.NOT_ACCEPTABLE)
except KeyError:
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
return make_response(f"Error bad key in {fields}",
HTTPStatus.BAD_REQUEST)
except ValueError as e:
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
class DataVarAPI(Resource):
def put(self):
preferred_mimetype = request.accept_mimetypes.best_match(
["application/octet-stream"]
)
["application/octet-stream"])
try:
if preferred_mimetype == "application/octet-stream":
filter_json = request.get_json()
filter = filter_json["filter"] if filter_json else None
return make_response(
current_app.data.data_frame_to_fbs_matrix(
filter, axis=Axis.VAR
),
HTTPStatus.OK,
{"Content-Type": "application/octet-stream"})
current_app.data.data_frame_to_fbs_matrix(filter,
axis=Axis.VAR),
HTTPStatus.OK, {"Content-Type": "application/octet-stream"})
else:
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
return make_response(
f"Unsupported MIME type '{request.accept_mimetypes}'",
HTTPStatus.NOT_ACCEPTABLE)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except ValueError as e:
@@ -167,43 +178,39 @@ class DataVarAPI(Resource):
class DiffExpObsAPI(Resource):
def post(self):
args = request.get_json()
# confirm mode is present and legal
try:
mode = DiffExpMode(args["mode"])
except KeyError:
return make_response("Error: mode is required", HTTPStatus.BAD_REQUEST)
return make_response("Error: mode is required",
HTTPStatus.BAD_REQUEST)
except ValueError:
return make_response(
f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST
)
return make_response(f"Error: invalid mode option {args['mode']}",
HTTPStatus.BAD_REQUEST)
# Validate filters
if mode == DiffExpMode.VAR_FILTER or "varFilter" in args:
# not NOT_IMPLEMENTED
return make_response(
"mode=varfilter not implemented", HTTPStatus.NOT_IMPLEMENTED
)
return make_response("mode=varfilter not implemented",
HTTPStatus.NOT_IMPLEMENTED)
if mode == DiffExpMode.TOP_N and "count" not in args:
return make_response(
"mode=topN requires a count parameter", HTTPStatus.BAD_REQUEST
)
return make_response("mode=topN requires a count parameter",
HTTPStatus.BAD_REQUEST)
if "set1" not in args:
return make_response("set1 is required.", HTTPStatus.BAD_REQUEST)
if Axis.VAR in args["set1"]["filter"]:
return make_response(
"Var filter not allowed for set1", HTTPStatus.BAD_REQUEST
)
return make_response("Var filter not allowed for set1",
HTTPStatus.BAD_REQUEST)
# set2
if "set2" not in args:
return make_response(
"Set2 as inverse of set1 is not implemented", HTTPStatus.NOT_IMPLEMENTED
)
return make_response("Set2 as inverse of set1 is not implemented",
HTTPStatus.NOT_IMPLEMENTED)
if Axis.VAR in args["set2"]["filter"]:
return make_response(
"Var filter not allowed for set2", HTTPStatus.BAD_REQUEST
)
return make_response("Var filter not allowed for set2",
HTTPStatus.BAD_REQUEST)
set1_filter = args["set1"]["filter"]
set2_filter = args.get("set2", {"filter": {}})["filter"]
@@ -219,13 +226,13 @@ class DiffExpObsAPI(Resource):
count,
current_app.data.features["diffexp"]["interactiveLimit"],
)
return make_response(
diffexp, HTTPStatus.OK, {"Content-Type": "application/json"}
)
return make_response(diffexp, HTTPStatus.OK,
{"Content-Type": "application/json"})
except (ValueError, FilterError) as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except InteractiveError:
return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
return make_response("Non-interactive request",
HTTPStatus.FORBIDDEN)
except JSONEncodingValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
@@ -235,17 +242,19 @@ class DiffExpObsAPI(Resource):
class LayoutObsAPI(Resource):
def get(self):
preferred_mimetype = request.accept_mimetypes.best_match(
["application/octet-stream"]
)
["application/octet-stream"])
try:
if preferred_mimetype == "application/octet-stream":
return make_response(current_app.data.layout_to_fbs_matrix(),
HTTPStatus.OK,
{"Content-Type": "application/octet-stream"})
return make_response(
current_app.data.layout_to_fbs_matrix(), HTTPStatus.OK,
{"Content-Type": "application/octet-stream"})
else:
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
return make_response(
f"Unsupported MIME type '{request.accept_mimetypes}'",
HTTPStatus.NOT_ACCEPTABLE)
except PrepareError as e:
return make_response(e.message, HTTPStatus.INTERNAL_SERVER_ERROR)
except ValueError as e: