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Code Issues Packages Projects Releases Wiki Activity

improve handling of non-finite floating point values (#490)

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* improve HTTP error reporting

* generate standards-compatible JSON

* add --nan-to-num work-around for non-finite floating point values

* lint

* update tests

* correctly set Infinities to min/max

* REAMDE update for --nan-to-num

* define constant for repetitive warning message

* clarify where NaN errors will occure
This commit is contained in:
Bruce Martin
2018-12-04 14:56:16 -08:00
committed by GitHub
parent 296ed752fa
commit 3bfeadc2b9
8 changed files with 138 additions and 47 deletions
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server/app/rest_api/rest.py
+54 -7
View File
@@ -1,5 +1,6 @@
from http import HTTPStatus
import pkg_resources
import warnings
from flask import (
Blueprint, current_app, jsonify, make_response, request
@@ -7,7 +8,7 @@ from flask import (
from flask_restful_swagger_2 import Api, swagger, Resource
from werkzeug.datastructures import ImmutableMultiDict
from server.app.util.constants import Axis, DiffExpMode
from server.app.util.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg
from server.app.util.filter import parse_filter, QueryStringError
from server.app.util.models import FilterModel
from server.app.util.utils import get_mime_type
@@ -160,7 +161,12 @@ class AnnotationsObsAPI(Resource):
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)
try:
return make_response(jsonify(annotation_response), HTTPStatus.OK)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
@swagger.doc({
"summary": "Fetch annotations (metadata) for filtered subset of observations.",
@@ -211,7 +217,12 @@ class AnnotationsObsAPI(Resource):
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)
try:
return make_response(jsonify(annotation_response), HTTPStatus.OK)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
class AnnotationsVarAPI(Resource):
@@ -253,7 +264,12 @@ class AnnotationsVarAPI(Resource):
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)
try:
return make_response(jsonify(annotation_response), HTTPStatus.OK)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
@swagger.doc({
"summary": "Fetch annotations (metadata) for filtered subset of variables.",
@@ -302,7 +318,12 @@ class AnnotationsVarAPI(Resource):
return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
except FilterError:
return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
return make_response(jsonify(annotation_response), HTTPStatus.OK)
try:
return make_response(jsonify(annotation_response), HTTPStatus.OK)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
class DataObsAPI(Resource):
@@ -363,6 +384,10 @@ class DataObsAPI(Resource):
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)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
@swagger.doc({
"summary": "Get data (expression values) from the dataframe.",
@@ -407,6 +432,10 @@ class DataObsAPI(Resource):
HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
class DataVarAPI(Resource):
@@ -465,6 +494,10 @@ class DataVarAPI(Resource):
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)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
@swagger.doc({
"summary": "Get data (expression values) from the dataframe.",
@@ -510,6 +543,10 @@ class DataVarAPI(Resource):
HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
class DiffExpObsAPI(Resource):
@@ -614,7 +651,12 @@ class DiffExpObsAPI(Resource):
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)
try:
return make_response(jsonify(diffexp), HTTPStatus.OK)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
class LayoutObsAPI(Resource):
@@ -647,7 +689,12 @@ class LayoutObsAPI(Resource):
layout = current_app.data.layout({})
except PrepareError as e:
return make_response(e.message, HTTPStatus.INTERNAL_SERVER_ERROR)
return make_response((jsonify({"layout": layout})), HTTPStatus.OK)
try:
return make_response((jsonify({"layout": layout})), HTTPStatus.OK)
except ValueError as e:
# JSON encoding failure, usually due to bad data
warnings.warn(JSON_NaN_to_num_warning_msg)
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
# @swagger.doc({
# "summary": "Observation layout for filtered subset.",