Merge pull request #184 from CitrineInformatics/maintain/json-fixes

Fix minor serialization bugs

gemd/json/gemd_encoder.py

@@ -1,4 +1,5 @@
 from json import JSONEncoder
+from uuid import UUID
 
 from gemd.entity.dict_serializable import DictSerializable
 from gemd.enumeration.base_enumeration import BaseEnumeration
@@ -13,5 +14,7 @@ def default(self, o):
             return o.as_dict()
         elif isinstance(o, BaseEnumeration):
             return o.value
+        elif isinstance(o, UUID):
+            return str(o)
         else:
             return JSONEncoder.default(self, o)

gemd/json/gemd_json.py

@@ -1,5 +1,6 @@
 import inspect
 from deprecation import deprecated
+from typing import Dict, Any, Type
 
 from gemd.entity.dict_serializable import DictSerializable
 from gemd.entity.base_entity import BaseEntity
@@ -21,7 +22,7 @@ class GEMDJson(object):
 
     def __init__(self, scope: str = 'auto'):
         self._scope = scope
-        self._clazz_index = DictSerializable.class_mapping
+        self._clazz_index = dict()
 
     @property
     def scope(self) -> str:
@@ -74,8 +75,15 @@ def loads(self, json_str: str, **kwargs):
         # Create an index to hold the objects by their uid reference
         # so we can replace links with pointers
         index = {}
+        clazz_index = DictSerializable.class_mapping
+        clazz_index.update(self._clazz_index)
         raw = json_builtin.loads(
-            json_str, object_hook=lambda x: self._load_and_index(x, index, True), **kwargs)
+            json_str,
+            object_hook=lambda x: self._load_and_index(x,
+                                                       index,
+                                                       clazz_index=clazz_index,
+                                                       substitute=True),
+            **kwargs)
         # the return value is in the 2nd position.
         return raw["object"]
 
@@ -196,8 +204,12 @@ def raw_loads(self, json_str, **kwargs):
         # Create an index to hold the objects by their uid reference
         # so we can replace links with pointers
         index = {}
+        clazz_index = DictSerializable.class_mapping
+        clazz_index.update(self._clazz_index)
         return json_builtin.loads(
-            json_str, object_hook=lambda x: self._load_and_index(x, index), **kwargs)
+            json_str,
+            object_hook=lambda x: self._load_and_index(x, index, clazz_index=clazz_index),
+            **kwargs)
 
     @deprecated(deprecated_in="1.13.0", removed_in="2.0.0",
                 details="Classes are now automatically registered when extending BaseEntity")
@@ -229,7 +241,12 @@ def register_classes(self, classes):
 
         self._clazz_index.update(classes)
 
-    def _load_and_index(self, d, object_index, substitute=False):
+    @staticmethod
+    def _load_and_index(
+            d: Dict[str, Any],
+            object_index: Dict[str, DictSerializable],
+            clazz_index: Dict[str, Type],
+            substitute: bool = False) -> DictSerializable:
         """
         Load the class based on the type string and index it, if a BaseEntity.
 
@@ -254,10 +271,10 @@ def _load_and_index(self, d, object_index, substitute=False):
             return d
         typ = d.pop("type")
 
-        if typ not in self._clazz_index:
+        if typ not in clazz_index:
             raise TypeError("Unexpected base object type: {}".format(typ))
 
-        clz = self._clazz_index[typ]
+        clz = clazz_index[typ]
         obj = clz.from_dict(d)
 
         if isinstance(obj, BaseEntity):  # Add it to the object index

gemd/json/tests/test_json.py

@@ -1,6 +1,7 @@
 """Test serialization and deserialization of gemd objects."""
 import json
 from copy import deepcopy
+from uuid import uuid4
 
 import pytest
 
@@ -10,6 +11,7 @@
 from gemd.entity.case_insensitive_dict import CaseInsensitiveDict
 from gemd.entity.attribute.condition import Condition
 from gemd.entity.attribute.parameter import Parameter
+from gemd.entity.dict_serializable import DictSerializable
 from gemd.entity.link_by_uid import LinkByUID
 from gemd.entity.object import MeasurementRun, MaterialRun, ProcessRun
 from gemd.entity.object import MeasurementSpec, MaterialSpec, ProcessSpec
@@ -51,14 +53,27 @@ def test_deserialize():
     """Round-trip serde should leave the object unchanged."""
     condition = Condition(name="A condition", value=NominalReal(7, ''))
     parameter = Parameter(name="A parameter", value=NormalReal(mean=17, std=1, units=''))
-    measurement = MeasurementRun("name", tags="A tag on a measurement", conditions=condition,
+    measurement = MeasurementRun("name",
+                                 tags="A tag on a measurement",
+                                 conditions=condition,
                                  parameters=parameter)
     copy_meas = GEMDJson().copy(measurement)
     assert(copy_meas.conditions[0].value == measurement.conditions[0].value)
     assert(copy_meas.parameters[0].value == measurement.parameters[0].value)
     assert(copy_meas.uids["auto"] == measurement.uids["auto"])
 
 
+def test_uuid_serde():
+    """Any UUIDs in uids & LinkByUIDs shouldn't break stuff."""
+    process = ProcessSpec(name="A process", uids={"uuid": uuid4(), "word": "turnbuckle"})
+    copy_proc = GEMDJson().copy(process)
+    assert all(copy_proc.uids[scope] == str(process.uids.get(scope)) for scope in copy_proc.uids)
+    assert len(copy_proc.uids) == len(process.uids)
+
+    link = LinkByUID(id=uuid4(), scope="mine")
+    assert GEMDJson().copy(link).id == str(link.id)
+
+
 def test_scope_control():
     """Serializing a nested object should be identical to individually serializing each piece."""
     input_material = MaterialSpec("input_material")
@@ -232,7 +247,12 @@ def test_pure_substitutions():
           ]
        '''
     index = {}
-    original = json.loads(json_str, object_hook=lambda x: GEMDJson()._load_and_index(x, index))
+    clazz_index = DictSerializable.class_mapping
+    original = json.loads(json_str,
+                          object_hook=lambda x: GEMDJson()._load_and_index(x,
+                                                                           index,
+                                                                           clazz_index)
+                          )
     frozen = deepcopy(original)
     loaded = substitute_objects(original, index)
     assert original == frozen

setup.py

@@ -2,7 +2,7 @@
 
 
 setup(name='gemd',
-      version='1.13.1',
+      version='1.13.2',
       url='http://github.com/CitrineInformatics/gemd-python',
       description="Python binding for Citrine's GEMD data model",
       author='Citrine Informatics',