Problem: model.py causes confusion

doc/source/api/cuds.rst

@@ -42,12 +42,12 @@ CUDS Computational Model
 
 .. autosummary::
 
-   ~model.CUDS
+   ~cuds.CUDS
    ~simulation.Simulation
 
 .. rubric:: Description
 
-.. automodule:: simphony.cuds.model
+.. automodule:: simphony.cuds.cuds
    :members:
    :undoc-members:
 

simphony/core/__init__.py

@@ -6,4 +6,5 @@
 class Default():
     pass
 
+
 __all__ = ['CUBA', 'DataContainer']

simphony/cuds/__init__.py

@@ -7,7 +7,7 @@
 from .lattice_items import LatticeNode
 from .particles import Particles
 from .particles_items import Particle, Bond
-from .model import CUDS
+from .cuds import CUDS
 from .simulation import Simulation
 from .meta import api
 

simphony/cuds/tests/test_materials.py

@@ -2,7 +2,7 @@
 import uuid
 from functools import partial
 
-from simphony.cuds.model import CUDS
+from simphony.cuds import CUDS
 from simphony.cuds.meta.api import Material
 from simphony.testing.utils import compare_material
 

simphony/io/serialisation.py

@@ -1,13 +1,13 @@
 import yaml
 import numpy
-
-from simphony.cuds.model import CUDS
-from simphony.cuds.meta.cuds_component import CUDSComponent
-from simphony.core.keywords import KEYWORDS
-# from simphony.cuds.meta import *
-from simphony.core.cuba import CUBA
+import uuid
 from collections import OrderedDict
 from importlib import import_module
+
+from simphony.core import CUBA
+from simphony.core.keywords import KEYWORDS
+from simphony.cuds import CUDS
+from simphony.cuds.meta.api import CUDSComponent
 from simphony.cuds.meta.validation import to_camel_case
 
 _CUDSREFMAP = OrderedDict()
@@ -91,7 +91,7 @@ def load_CUDS(handle):
 
     """
 
-    comp_dict = {}
+    cuds_components = {}
     name = None
     desc = None
     for data in yaml.safe_load_all(handle):
@@ -104,11 +104,11 @@ def load_CUDS(handle):
                 desc = dict_cuds['DESCRIPTION']
             else:
                 _dict_to_CUDSComponent(cubatype, dict_cuds[cubatype],
-                                       comp_dict)
+                                       cuds_components)
 
     model = CUDS(name=name, description=desc)
-    for compid in comp_dict.keys():
-        model.add(comp_dict[compid])
+    for comp in cuds_components.values():
+        model.add(comp)
 
     return model
 
@@ -147,11 +147,8 @@ def _CUDSComponent_to_yaml(comp, stream):
     # Go through the keys in the component
     cdata = comp._data
     for key in cdata.keys():
-        # Skip the UID key, as it's not accepted by the deserializer
-        if key == CUBA.UID:
-            continue
         # Check if the data is a list or numpy types or CUDSComponents
-        elif type(cdata[key]) == list:
+        if type(cdata[key]) == list:
             # List of simple types?
             if KEYWORDS[key._name_].dtype in [numpy.float64,
                                               numpy.int32, bool]:
@@ -210,7 +207,7 @@ def _CUDSComponent_to_yaml(comp, stream):
     return stream
 
 
-def _dict_to_CUDSComponent(cubatype, comp, comp_dict={}):
+def _dict_to_CUDSComponent(cubatype, comp, comp_dict=None):
     """ Generate a CUDSComponent on the basis of a dictionary
     provided by PyYaml library.
 
@@ -226,12 +223,16 @@ def _dict_to_CUDSComponent(cubatype, comp, comp_dict={}):
             id(CUDSComponent): CUDSComponent
 
     """
-
+    if comp_dict is None:
+        comp_dict = {}
     # Check that comp does not refer to one of the components that
     # have been already constructed
     if id(comp) in comp_dict.keys():
         return
 
+    # Pop out uid, since we need to set it differently.
+    uid = comp.pop('UID')
+
     if cubatype in KEYWORDS.keys():
         # Find corresponding module and instantiate the class
         mod = import_module('simphony.cuds.meta.%s' % cubatype.lower())
@@ -245,8 +246,7 @@ def _dict_to_CUDSComponent(cubatype, comp, comp_dict={}):
         system_managed_keys = {}
         supp_params = [str(e).replace('CUBA.', '')
                        for e in comp_class.supported_parameters()]
-        # Don't accept UUID entry from the yaml file
-        supp_params.remove('UID')
+
         for key in comp.keys():
             # Check if the key is supported
             if key in supp_params:
@@ -290,6 +290,9 @@ def _dict_to_CUDSComponent(cubatype, comp, comp_dict={}):
         # Add system managed components by updating the DataContainer
         data = comp_inst.data
         data.update(system_managed_keys)
+
+        # Set the initial uid
+        data[CUBA.UID] = uuid.UUID(uid)
         comp_inst.data = data
     else:
         message = 'Unknown CUDSComponent "{}"'
@@ -298,3 +301,5 @@ def _dict_to_CUDSComponent(cubatype, comp, comp_dict={}):
     # Store component under the key representing it's memory location
     # so that correct object references from the yaml file are preserved
     comp_dict[id(comp)] = comp_inst
+
+    return comp_dict

simphony/io/tests/test_serialisation.py

@@ -8,10 +8,10 @@
 import tempfile
 import uuid
 
-from simphony.cuds.meta.cuds_component import CUDSComponent
-from simphony.cuds.meta.material import Material
-from simphony.cuds.meta.material_relation import MaterialRelation
-from simphony.cuds.model import CUDS
+from simphony.cuds.meta.api import CUDSComponent
+from simphony.cuds.meta.api import Material
+from simphony.cuds.meta.api import MaterialRelation
+from simphony.cuds import CUDS
 from simphony.io.serialisation import save_CUDS, load_CUDS
 
 
@@ -62,8 +62,8 @@ def test_save_CUDS_empty(self):
 
     def test_save_CUDS_complicated_data(self):
         filename = os.path.join(self.temp_dir, 'test_full.yml')
-        C = CUDS(name='full',
-                 description='model with crossreferenced components')
+        cuds = CUDS(name='full',
+                    description='model with crossreferenced components')
 
         M1 = Material(name='steel',
                       description='FCC steel sphere structure')
@@ -74,31 +74,42 @@ def test_save_CUDS_complicated_data(self):
         MR2 = MaterialRelation(name='epoxy in sheet metal container',
                                material=[M2, M3])
         # M1 is not added
-        C.add(M2)
-        C.add(M3)
-        C.add(MR1)
-        C.add(MR2)
+        cuds.add(M2)
+        cuds.add(M3)
+        cuds.add(MR1)
+        cuds.add(MR2)
 
         with closing(open(filename, 'w')) as handle:
-            save_CUDS(handle, C)
+            save_CUDS(handle, cuds)
+            print("cuds data", cuds.data)
 
         with closing(open(filename, 'r')) as handle:
-            CC = load_CUDS(handle)
+            loaded_cuds = load_CUDS(handle)
+            print("loaded_cuds data", loaded_cuds.data)
 
-        self.assertEqual(CC.name, C.name)
-        self.assertEqual(CC.description, C.description)
+        self.assertEqual(loaded_cuds.name, cuds.name)
+        self.assertEqual(loaded_cuds.description, cuds.description)
+
+        for cuds_item in cuds.iter(CUDSComponent):
+            print('item original', cuds_item)
+
+        for cuds_item in loaded_cuds.iter(CUDSComponent):
+            print('item loaded', cuds_item)
 
         # Iterate over components in the original model and check
         # that they are present in the loaded model. Loaded model
         # has additionally material 'M1' included.
-        for Citem in C.iter(CUDSComponent):
+        for cuds_item in cuds.iter(CUDSComponent):
             # Check items that have name parameter defined
-            if Citem.name is not None:
-                CCitem = CC.get(Citem.name)
-                for key in Citem.data.keys():
-                    Ci = Citem.data[key]
-                    CCi = CCitem.data[key]
-                    _compare_components(Ci, CCi, testcase=self)
+            print("cuds_item", cuds_item)
+            if cuds_item.name is not None:
+                loaded_item = loaded_cuds.get_by_uid(cuds_item.uid)
+                print("loaded_item", loaded_item)
+                for key in cuds_item.data.keys():
+                    print(key)
+                    ci = cuds_item.data[key]
+                    li = loaded_item.data[key]
+                    _compare_components(ci, li, testcase=self)
 
 
 def _compare_components(comp1, comp2, testcase):