Move jsonification to engine level (#511)

server/app/util/constants.py

@@ -3,6 +3,9 @@ from enum import Enum
 
 DEFAULT_TOP_N = 10
 
+# response mimetypes
+JSON_MIMETYPE = "application/json"
+
 
 class AugmentedEnum(Enum):
     def __hash__(self):
@@ -27,4 +30,6 @@ class DiffExpMode(AugmentedEnum):
     VAR_FILTER = "varFilter"
 
 
-JSON_NaN_to_num_warning_msg = "JSON encoding failure - suggest trying --nan-to-num command line option"
+JSON_NaN_to_num_warning_msg = (
+    "JSON encoding failure - suggest trying --nan-to-num command line option"
+)

server/app/util/errors.py

@@ -16,6 +16,15 @@ class InteractiveError(Exception):
         self.message = message
 
 
+class JSONEncodingValueError(Exception):
+    """
+    Raised when file loaded into scanpy is misformatted
+    """
+
+    def __init__(self, message):
+        self.message = message
+
+
 class MimeTypeError(Exception):
     """
     Raised when incompatible MIME type selected

server/app/util/utils.py

@@ -54,3 +54,7 @@ def whole_number(value):
     if value < 0:
         raise ArgumentTypeError(f"{value} is not >= 0")
     return value
+
+
+def jsonify_scanpy(data):
+    return json.dumps(data, cls=Float32JSONEncoder, allow_nan=False)