Merge pull request #106 from CitrineInformatics/feature/scope-control

Added control for default scope in serialization

gemd/json/gemd_json.py

@@ -47,6 +47,8 @@ class GEMDJson(object):
 
     The serialization and deserialization strategy implemented by this class is described in
     :ref:`Serialization In Depth`
+
+    scope: defines the scope to use for autogenerated UUIDs for objects without uids
     """
 
     _clazzes = [
@@ -65,12 +67,18 @@ class GEMDJson(object):
 
     _link_type = LinkByUID
 
-    def __init__(self):
+    def __init__(self, scope='auto'):
+        self._scope = scope
         self._clazz_index = {}
         # build index from the class's typ member to the class itself
         for clazz in self._clazzes:
             self._clazz_index[clazz.typ] = clazz
 
+    @property
+    def scope(self):
+        """Return the default scope value."""
+        return self._scope
+
     def dumps(self, obj, **kwargs):
         """
         Serialize a gemd object, or container of them, into a json-formatting string.
@@ -90,7 +98,8 @@ def dumps(self, obj, **kwargs):
         """
         # create a top level list of [flattened_objects, link-i-fied return value]
         res = {"object": obj}
-        additional = flatten(res)
+
+        additional = flatten(res, self.scope)
         res = substitute_links(res)
         res["context"] = additional
         return json_builtin.dumps(res, cls=GEMDEncoder, sort_keys=True, **kwargs)
@@ -214,7 +223,7 @@ def thin_dumps(self, obj, **kwargs):
             A serialized string of `obj`, with link_by_uid in place of pointers to other objects.
 
         """
-        set_uuids(obj)
+        set_uuids(obj, self.scope)
         res = substitute_links(obj)
         return json_builtin.dumps(res, cls=GEMDEncoder, sort_keys=True, **kwargs)
 

gemd/json/tests/test_json.py

@@ -60,6 +60,33 @@ def test_deserialize():
     assert(copy_meas.uids["auto"] == measurement.uids["auto"])
 
 
+def test_scope_control():
+    """Serializing a nested object should be identical to individually serializing each piece."""
+    input_material = MaterialSpec()
+    process = ProcessSpec()
+    IngredientSpec(material=input_material, process=process)
+    material = MaterialSpec(process=process)
+
+    # Verify the default scope is there
+    default_json = GEMDJson()
+    default_text = default_json.dumps(material)
+    assert "auto" in default_text
+    assert "custom" not in default_text
+
+    # Clear out ids
+    input_material.uids = {}
+    process.uids = {}
+    process.ingredients[0].uids = {}
+    input_material.uids = {}
+    material.uids = {}
+
+    # Verify the default scope is there
+    custom_json = GEMDJson(scope='custom')
+    custom_text = custom_json.dumps(material)
+    assert "auto" not in custom_text
+    assert "custom" in custom_text
+
+
 def test_deserialize_extra_fields():
     """Extra JSON fields should be ignored in deserialization."""
     json_data = '{"context": [],' \

gemd/util/impl.py

@@ -8,18 +8,18 @@
 from toolz import concatv
 
 
-def set_uuids(obj, name="auto"):
+def set_uuids(obj, scope):
     """
     Recursively assign a uuid to every BaseEntity that doesn't already contain a uuid.
 
     This ensures that all of the pointers in the object can be replaced with LinkByUID objects
     :param obj: to recursively assign uuids to
-    :param name: of the uuid to assign (default: "auto")
+    :param scope: of the uuid to assign
     :return: None
     """
     def func(base_obj):
         if len(base_obj.uids) == 0:
-            base_obj.add_uid(name, str(uuid.uuid4()))
+            base_obj.add_uid(scope, str(uuid.uuid4()))
         return
     recursive_foreach(obj, func)
     return
@@ -105,7 +105,7 @@ def substitute_objects(obj, index):
                        applies=lambda o: isinstance(o, LinkByUID))
 
 
-def flatten(obj):
+def flatten(obj, scope):
     """
     Flatten a BaseEntity into a list of objects connected by LinkByUID objects.
 
@@ -119,11 +119,12 @@ def flatten(obj):
     ingredients of the process in the result, even though process.ingredients is skipped.
     This supports the flattening of entire material histories.
 
-    :param obj: defining the scope of the flatten
+    :param obj: the object where the graph traversal starts
+    :param scope: the scope of the autogenerated ids
     :return: a list of BaseEntity with LinkByUIDs to any BaseEntity members
     """
     # The ids should be set in the actual object so they are consistent
-    set_uuids(obj)
+    set_uuids(obj, scope)
 
     # list of uids that we've seen, to avoid returning duplicates
     known_uids = set()

gemd/util/tests/test_flatten.py

@@ -15,7 +15,7 @@ def test_flatten_bounds():
     )
     spec = ProcessSpec(name="spec", template=template)
 
-    flat = flatten(spec)
+    flat = flatten(spec, 'test-scope')
     assert len(flat) == 2, "Expected 2 flattened objects"
 
 
@@ -31,15 +31,16 @@ def test_flatten_empty_history():
     transform_run = ProcessRun(name="transformed", spec=transform)
     ingredient_run = IngredientRun(material=input_run, process=transform_run, spec=ingredient)
 
-    assert len(flatten(procured)) == 1
-    assert len(flatten(input)) == 1
-    assert len(flatten(ingredient)) == 3
-    assert len(flatten(transform)) == 3
+    assert len(flatten(procured, 'test-scope')) == 1
+    assert 'test-scope' in procured.uids
+    assert len(flatten(input, 'test-scope')) == 1
+    assert len(flatten(ingredient, 'test-scope')) == 3
+    assert len(flatten(transform, 'test-scope')) == 3
 
-    assert len(flatten(procured_run)) == 3
-    assert len(flatten(input_run)) == 3
-    assert len(flatten(ingredient_run)) == 7
-    assert len(flatten(transform_run)) == 7
+    assert len(flatten(procured_run, 'test-scope')) == 3
+    assert len(flatten(input_run, 'test-scope')) == 3
+    assert len(flatten(ingredient_run, 'test-scope')) == 7
+    assert len(flatten(transform_run, 'test-scope')) == 7
 
 
 def test_flatmap_unidirectional_ordering():

setup.py

@@ -36,7 +36,7 @@ def run(self):
 
 
 setup(name='gemd',
-      version='0.7.4',
+      version='0.8.0',
       url='http://github.com/CitrineInformatics/gemd-python',
       description="Python binding for Citrine's GEMD data model",
       author='Max Hutchinson',