core library (#711)

* move app creation to function

* create engine without load

* flake 8 fixes

* cleanup original scanpy test

* add default config

* handle missing data

* test data changes

* unify update

* load data isn't static anymore

* make app a class

server/app/util/constants.py

@@ -30,3 +30,4 @@ class DiffExpMode(AugmentedEnum):
 JSON_NaN_to_num_warning_msg = (
     "JSON encoding failure - please verify all data are finite values (no NaN or Infinities)"
 )
+REACTIVE_LIMIT = 1_000_000

server/app/util/errors.py

@@ -50,3 +50,12 @@ class ScanpyFileError(Exception):
 
     def __init__(self, message):
         self.message = message
+
+
+class DriverError(Exception):
+    """
+    Raised when file loaded into scanpy is misformatted
+    """
+
+    def __init__(self, message):
+        self.message = message

server/app/util/utils.py

@@ -1,6 +1,10 @@
+from functools import wraps
+
 from flask import json
 from numpy import float32, integer
 
+from server.app.util.errors import DriverError
+
 
 class Float32JSONEncoder(json.JSONEncoder):
     def __init__(self, *args, **kwargs):
@@ -28,3 +32,12 @@ def custom_format_warning(msg, *args, **kwargs):
 
 def jsonify_scanpy(data):
     return json.dumps(data, cls=Float32JSONEncoder, allow_nan=False)
+
+
+def requires_data(func):
+    @wraps(func)
+    def wrapped_function(self, *args, **kwargs):
+        if self.data is None:
+            raise DriverError(f"error data must be loaded before you call {func.__name__}")
+        return func(self, *args, **kwargs)
+    return wrapped_function