The following code is executed when running a spatial method locally (not from a web service) on an ArcGIS Geometry object:
if HASARCPY:
if isinstance(second_geometry, Geometry):
second_geometry = second_geometry.as_arcpy
return self.as_arcpy.intersect(other=second_geometry,
dimension=dimension)
elif HASSHAPELY:
if isinstance(second_geometry, Geometry):
second_geometry = second_geometry.as_shapely
return Geometry(self.as_shapely.intersection(
other=second_geometry).__geo_interface__)
return None
If ArcPy is installed, it is used to run the spatial method while Shapely is used if ArcPy is not installed. I don't have time to dig deeper right now, but I suspect the issue is line #8 because an invalid geometry is being returned to second_geometry.
UPDATE: There is a bug in the __geo_interface__ methods of the API. When ArcPy is installed, the API lets ArcPy handle __geo_interface__ calls, but the API uses native code (the code with a bug) when ArcPy is not installed. The following is from a Python interpreter without access to ArcPy:
Python 3.5.3 |Continuum Analytics, Inc.| (default, May 15 2017, 10:43:23) [MSC v.1900 64 bit (AMD64)] on win32
>>> from arcgis.geometry import Geometry
>>> from pprint import pprint
>>>
>>>
... json = {
... "rings": [
... [
... [0, 0],
... [10, 10],
... [0, 10],
... [10, 10],
... [10, 0],
... [0, 0]
... ],
... [
... [3, 3],
... [7, 3],
... [7, 7],
... [3, 7],
... [3, 3]
... ]
... ],
... "spatialReference": {
... "wkid": 3857
... }
... }
>>> pprint(json)
{'rings': [[[0, 0], [10, 10], [0, 10], [10, 10], [10, 0], [0, 0]],
[[3, 3], [7, 3], [7, 7], [3, 7], [3, 3]]],
'spatialReference': {'wkid': 3857}}
>>>
>>> pprint(Geometry(json).__geo_interface__)
{'coordinates': [[[(0, 0), (10, 10), (0, 10), (10, 10), (10, 0), (0, 0)]],
[[(3, 3), (7, 3), (7, 7), (3, 7), (3, 3)]]],
'type': 'MultiPolygon'}
>>>
If you treat round and square brackets the same, which they are for __geo_interface__ purposes, you will notice the API has inserted an extra closing bracket on the outer coordinates. The extra closing bracket converts the geometry from a polygon with a hole in it to a multi-part polygon with overlapping parts, hence the errors you are seeing in Shapely.
