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Code Issues Packages Projects Releases Wiki Activity

Filter in engine (#307)

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* Add empty filter case

* Filtering dataframes moved to engine instead of rest

* minor changes from PR review

* Minor fixes from PR review

Pass {} instead of none if no filter
chain exceptions
typos
This commit is contained in:
Charlotte Weaver
2018-10-11 15:23:31 -07:00
committed by GitHub
parent ee0b066eb6
commit 210787cb5d
5 changed files with 127 additions and 93 deletions
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server/app/rest_api/rest.py
+46 -48
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@@ -10,7 +10,7 @@ from werkzeug.datastructures import ImmutableMultiDict
from server.app.util.constants import Axis, DiffExpMode
from server.app.util.filter import parse_filter, QueryStringError
from server.app.util.models import FilterModel
from server.app.util.utils import MimeTypeError, get_mime_type
from server.app.util.utils import FilterError, InteractiveError, MimeTypeError, get_mime_type
"""
Sort order for routes
@@ -153,7 +153,7 @@ class AnnotationsObsAPI(Resource):
def get(self):
fields = request.args.getlist("annotation-name", None)
try:
annotation_response = current_app.data.annotation(current_app.data.data, "obs", fields)
annotation_response = current_app.data.annotation({}, "obs", fields)
except KeyError:
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
return make_response(jsonify(annotation_response), HTTPStatus.OK)
@@ -202,13 +202,11 @@ class AnnotationsObsAPI(Resource):
def put(self):
fields = request.args.getlist("annotation-name", None)
try:
df = current_app.data.filter_dataframe(request.get_json()["filter"], include_uns=False)
except KeyError:
return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
try:
annotation_response = current_app.data.annotation(df, "obs", fields)
annotation_response = current_app.data.annotation(request.get_json()["filter"], "obs", fields)
except KeyError:
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
return make_response(jsonify(annotation_response), HTTPStatus.OK)
@@ -248,7 +246,7 @@ class AnnotationsVarAPI(Resource):
def get(self):
fields = request.args.getlist("annotation-name", None)
try:
annotation_response = current_app.data.annotation(current_app.data.data, "var", fields)
annotation_response = current_app.data.annotation({}, "var", fields)
except KeyError:
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
return make_response(jsonify(annotation_response), HTTPStatus.OK)
@@ -295,13 +293,11 @@ class AnnotationsVarAPI(Resource):
def put(self):
fields = request.args.getlist("annotation-name", None)
try:
df = current_app.data.filter_dataframe(request.get_json()["filter"], include_uns=False)
except KeyError:
return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
try:
annotation_response = current_app.data.annotation(df, "var", fields)
annotation_response = current_app.data.annotation(request.get_json()["filter"], "var", fields)
except KeyError:
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
except FilterError as e:
return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
return make_response(jsonify(annotation_response), HTTPStatus.OK)
@@ -352,10 +348,6 @@ class DataObsAPI(Resource):
filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])
except QueryStringError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
try:
df = current_app.data.filter_dataframe(filter_, include_uns=False)
except KeyError:
return make_response("malformed filter", HTTPStatus.BAD_REQUEST)
# TODO support CSV
try:
# TODO store mime_type when more than one is supported
@@ -363,7 +355,10 @@ class DataObsAPI(Resource):
header=request.accept_mimetypes)
except MimeTypeError as e:
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.OBS))), HTTPStatus.OK)
try:
return make_response((jsonify(current_app.data.data_frame(filter_, axis=Axis.OBS))), HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
@swagger.doc({
"summary": "Get data (expression values) from the dataframe.",
@@ -399,15 +394,15 @@ class DataObsAPI(Resource):
def put(self):
if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
try:
df = current_app.data.filter_dataframe(request.get_json()["filter"], include_uns=False)
except KeyError:
return make_response("malformed filter", HTTPStatus.BAD_REQUEST)
try:
get_mime_type(acceptable_types=["application/json"], header=request.accept_mimetypes)
except MimeTypeError as e:
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.OBS))), HTTPStatus.OK)
try:
return make_response((jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.OBS))),
HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
class DataVarAPI(Resource):
@@ -457,16 +452,15 @@ class DataVarAPI(Resource):
filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])
except QueryStringError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
try:
df = current_app.data.filter_dataframe(filter_, include_uns=False)
except KeyError:
return make_response("malformed filter", HTTPStatus.BAD_REQUEST)
try:
get_mime_type(acceptable_types=["application/json"], query_param=accept_type,
header=request.accept_mimetypes)
except MimeTypeError as e:
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.VAR))), HTTPStatus.OK)
try:
return make_response((jsonify(current_app.data.data_frame(filter_, axis=Axis.VAR))), HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
@swagger.doc({
"summary": "Get data (expression values) from the dataframe.",
@@ -502,16 +496,16 @@ class DataVarAPI(Resource):
def put(self):
if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
try:
df = current_app.data.filter_dataframe(request.get_json()["filter"], include_uns=False)
except KeyError:
return make_response("malformed filter", HTTPStatus.BAD_REQUEST)
# TODO support CSV
try:
get_mime_type(acceptable_types=["application/json"], header=request.accept_mimetypes)
except MimeTypeError as e:
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.VAR))), HTTPStatus.OK)
try:
return make_response((jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.VAR))),
HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
class DiffExpObsAPI(Resource):
@@ -605,18 +599,15 @@ class DiffExpObsAPI(Resource):
if "varFilter" in args:
set1_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
set2_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
df1 = current_app.data.filter_dataframe(set1_filter, include_uns=False)
# TODO inverse
df2 = current_app.data.filter_dataframe(set2_filter, include_uns=False)
# exceeds size limit
if df1.shape[0] + df2.shape[0] > current_app.data.features["diffexp"]["interactiveLimit"]:
return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
# mode
count = args.get("count", None)
try:
diffexp = current_app.data.diffexp(df1, df2, count)
except ValueError as ve:
return make_response(ve.message, HTTPStatus.BAD_REQUEST)
diffexp = current_app.data.diffexp(set1_filter, set2_filter, count,
current_app.data.features["diffexp"]["interactiveLimit"])
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(jsonify(diffexp), HTTPStatus.OK)
@@ -643,7 +634,7 @@ class LayoutObsAPI(Resource):
}
})
def get(self):
return make_response((jsonify({"layout": current_app.data.layout(current_app.data.data)})), HTTPStatus.OK)
return make_response((jsonify({"layout": current_app.data.layout({})})), HTTPStatus.OK)
@swagger.doc({
"summary": "Observation layout for filtered subset.",
@@ -681,12 +672,19 @@ class LayoutObsAPI(Resource):
})
def post(self):
try:
df = current_app.data.filter_dataframe(request.get_json()["filter"])
except KeyError:
return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
if len(df.obs.index) > current_app.data.features["layout"]["obs"]["interactiveLimit"]:
return make_response(
jsonify({
"layout": current_app.data.layout(
request.get_json()["filter"],
interactive_limit=current_app.data.features["layout"]["obs"]["interactiveLimit"]
)
}),
HTTPStatus.OK
)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except InteractiveError:
return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
return make_response((jsonify({"layout": current_app.data.layout(df)})), HTTPStatus.OK)
def get_api_resources():