Merge pull request #69 from CitrineInformatics/release/0.4.0

Release/0.4.0

Author: bfolie

.gitignore

@@ -49,6 +49,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+flex_measurements.json
 
 # Translations
 *.mo

.travis.yml

@@ -7,8 +7,9 @@ install:
 - pip install -U -r test_requirements.txt
 - pip install --no-deps -e .
 script:
-- pytest --flake8 --cov=taurus --cov-report term-missing --cov-report term:skip-covered --cov-config=tox.ini
+- pytest --cov=taurus --cov-report term-missing --cov-report term:skip-covered --cov-config=tox.ini
   --cov-fail-under=100 -s -r ./taurus
+- flake8 taurus
 - cd docs; make html; cd ..;
 - touch ./docs/_build/html/.nojekyll
 deploy:

taurus/client/json_encoder.py

@@ -37,7 +37,7 @@
 from taurus.entity.value.uniform_integer import UniformInteger
 from taurus.entity.value.uniform_real import UniformReal
 from taurus.enumeration.base_enumeration import BaseEnumeration
-from taurus.util import flatten, substitute_links, deepcopy, set_uuids, substitute_objects
+from taurus.util import flatten, substitute_links, set_uuids, substitute_objects
 
 
 def dumps(obj, **kwargs):
@@ -60,7 +60,7 @@ def dumps(obj, **kwargs):
     # create a top level list of [flattened_objects, link-i-fied return value]
     res = [obj]
     additional = flatten(res)
-    substitute_links(res)
+    res = substitute_links(res)
     res.insert(0, additional)
     return json.dumps(res, cls=TaurusEncoder, sort_keys=True, **kwargs)
 
@@ -88,8 +88,8 @@ def loads(json_str, **kwargs):
     index = {}
     raw = json.loads(json_str, object_hook=lambda x: _loado(x, index), **kwargs)
     # the return value is in the 2nd position.
-    substitute_objects(raw, index)
-    return raw[1]
+    subbed = substitute_objects(raw, index)
+    return subbed[1]
 
 
 def load(fp, **kwargs):
@@ -140,8 +140,8 @@ def thin_dumps(obj, **kwargs):
 
     Parameters
     ----------
-    obj: BaseEntity
-        Object to dump (must be a BaseEntity because it must have uids)
+    obj:
+        Object to dump
     **kwargs: keyword args, optional
         Optional keyword arguments to pass to `json.dumps()`.
 
@@ -151,12 +151,8 @@ def thin_dumps(obj, **kwargs):
         A serialized string of `obj`, with link_by_uid in place of pointers to other objects.
 
     """
-    if not isinstance(obj, BaseEntity):
-        raise TypeError("Can only dump BaseEntities, but got {}".format(type(obj)))
-
     set_uuids(obj)
-    res = deepcopy(obj)
-    substitute_links(res)
+    res = substitute_links(obj)
     return json.dumps(res, cls=TaurusEncoder, sort_keys=True, **kwargs)
 
 

taurus/client/tests/test_json.py

@@ -1,8 +1,12 @@
 """Test serialization and deserialization of taurus objects."""
 import json
+from copy import deepcopy
+
 import pytest
 
-from taurus.client.json_encoder import dumps, loads, copy, thin_dumps
+from taurus.client.json_encoder import dumps, loads, copy, thin_dumps, _loado
+from taurus.entity.attribute.property import Property
+from taurus.entity.bounds.real_bounds import RealBounds
 from taurus.entity.dict_serializable import DictSerializable
 from taurus.entity.case_insensitive_dict import CaseInsensitiveDict
 from taurus.entity.attribute.condition import Condition
@@ -11,10 +15,12 @@
 from taurus.entity.object import MeasurementRun, MaterialRun, ProcessRun, MeasurementSpec
 from taurus.entity.object.ingredient_run import IngredientRun
 from taurus.entity.object.ingredient_spec import IngredientSpec
+from taurus.entity.template.property_template import PropertyTemplate
 from taurus.entity.value.nominal_integer import NominalInteger
 from taurus.entity.value.nominal_real import NominalReal
 from taurus.entity.value.normal_real import NormalReal
 from taurus.enumeration.origin import Origin
+from taurus.util import substitute_objects, substitute_links
 
 
 def test_serialize():
@@ -66,8 +72,24 @@ def test_enumeration_serde():
     assert copy_condition.notes == Origin.get_value(condition.notes)
 
 
+def test_attribute_serde():
+    """An attribute with a link to an attribute template should be copy-able."""
+    prop_tmpl = PropertyTemplate(name='prop_tmpl',
+                                 bounds=RealBounds(0, 2, 'm')
+                                 )
+    prop = Property(name='prop',
+                    template=prop_tmpl,
+                    value=NominalReal(1, 'm')
+                    )
+    meas_spec = MeasurementSpec("a spec")
+    meas = MeasurementRun("a measurement", spec=meas_spec, properties=[prop])
+    assert loads(dumps(prop)) == prop
+    assert loads(dumps(meas)) == meas
+    assert isinstance(prop.template, PropertyTemplate)
+
+
 def test_thin_dumps():
-    """Test that thin_dumps turns pointers into links and doesn't work on non-BaseEntity."""
+    """Test that thin_dumps turns pointers into links."""
     mat = MaterialRun("The actual material")
     meas_spec = MeasurementSpec("measurement", uids={'my_scope': '324324'})
     meas = MeasurementRun("The measurement", spec=meas_spec, material=mat)
@@ -78,8 +100,13 @@ def test_thin_dumps():
     assert isinstance(thin_copy.spec, LinkByUID)
     assert thin_copy.spec.id == meas_spec.uids['my_scope']
 
+    # Check that LinkByUID objects are correctly converted their JSON equivalent
+    expected_json = '{"id": "my_id", "scope": "scope", "type": "link_by_uid"}'
+    assert thin_dumps(LinkByUID('scope', 'my_id')) == expected_json
+
+    # Check that objects lacking .uid attributes will raise an exception when dumped
     with pytest.raises(TypeError):
-        thin_dumps(LinkByUID('scope', 'id'))
+        thin_dumps({{'key': 'value'}})
 
 
 def test_uid_deser():
@@ -126,6 +153,50 @@ def __init__(self, foo):
         loads(serialized)
 
 
+def test_pure_subsitutions():
+    """Make sure substitute methods don't mutate inputs."""
+    json_str = '''
+          [
+            [
+              {
+                "uids": {
+                  "id": "9118c2d3-1c38-47fe-a650-c2b92fdb6777"
+                },
+                "type": "material_run",
+                "name": "flour"
+              }
+            ],
+            {
+              "type": "ingredient_run",
+              "uids": {
+                "id": "8858805f-ec02-49e4-ba3b-d784e2aea3f8"
+              },
+              "material": {
+                "type": "link_by_uid",
+                "scope": "ID",
+                "id": "9118c2d3-1c38-47fe-a650-c2b92fdb6777"
+              },
+              "process": {
+                "type": "link_by_uid",
+                "scope": "ID",
+                "id": "9148c2d3-2c38-47fe-b650-c2b92fdb6777"
+              }
+            }
+          ]
+       '''
+    index = {}
+    original = json.loads(json_str, object_hook=lambda x: _loado(x, index))
+    frozen = deepcopy(original)
+    loaded = substitute_objects(original, index)
+    assert original == frozen
+    frozen_loaded = deepcopy(loaded)
+    substitute_links(loaded)
+    assert loaded == frozen_loaded
+    for o in loaded:
+        substitute_links(o)
+    assert loaded == frozen_loaded
+
+
 def test_case_insensitive_rehydration():
     """