Merge pull request #363 from fschrader1992/master

Validation Updates

Author: mpsonntag

odml/property.py

@@ -6,6 +6,7 @@
 
 from . import base
 from . import dtypes
+from . import validation
 from . import format as frmt
 from .tools.doc_inherit import inherit_docstring, allow_inherit_docstring
 
@@ -128,6 +129,11 @@ def __init__(self, name=None, values=None, parent=None, unit=None,
 
         self.parent = parent
 
+        for err in validation.Validation(self).errors:
+            if err.is_error:
+                msg = "\n\t- %s %s: %s" % (err.obj, err.rank, err.msg)
+                print(msg)
+
     def __len__(self):
         return len(self._values)
 

odml/section.py

@@ -12,6 +12,7 @@
 from . import base
 from . import format as fmt
 from . import terminology
+from . import validation
 from .doc import BaseDocument
 # this is supposedly ok, as we only use it for an isinstance check
 from .property import BaseProperty
@@ -81,6 +82,11 @@ def __init__(self, name=None, type=None, parent=None,
         self.type = type
         self.parent = parent
 
+        for err in validation.Validation(self).errors:
+            if err.is_error:
+                msg = "\n\t- %s %s: %s" % (err.obj, err.rank, err.msg)
+                print(msg)
+
     def __repr__(self):
         return "Section[%d|%d] {name = %s, type = %s, id = %s}" % (len(self._sections),
                                                                    len(self._props),

odml/validation.py

@@ -3,6 +3,8 @@
 Generic odML validation framework.
 """
 
+from . import dtypes
+
 LABEL_ERROR = 'error'
 LABEL_WARNING = 'warning'
 
@@ -74,12 +76,16 @@ def register_handler(klass, handler):
         """
         Validation._handlers.setdefault(klass, set()).add(handler)
 
-    def __init__(self, doc):
-        self.doc = doc  # may also be a section
+    def __init__(self, obj):
+        self.doc = obj  # may also be a section
         self.errors = []
-        self.validate(doc)
 
-        for sec in doc.itersections(recursive=True):
+        self.validate(obj)
+
+        if obj.format().name == "property":
+            return
+
+        for sec in obj.itersections(recursive=True):
             self.validate(sec)
             for prop in sec.properties:
                 self.validate(prop)
@@ -116,6 +122,31 @@ def __getitem__(self, obj):
 # ------------------------------------------------
 # validation rules
 
+def object_required_attributes(obj):
+    """
+    Tests that no Object has undefined attributes, given in format.
+
+    :param obj: document, section or property.
+    """
+
+    args = obj.format().arguments
+    for arg in args:
+        if arg[1] == 1:
+            if not hasattr(obj, arg[0]):
+                msg = "Missing attribute %s for %s" % (obj.format().name.capitalize(), arg[0])
+                yield ValidationError(obj, msg, LABEL_ERROR)
+                continue
+            obj_arg = getattr(obj, arg[0])
+            if not obj_arg and not isinstance(obj_arg, bool):
+                msg = "%s %s undefined" % (obj.format().name.capitalize(), arg[0])
+                yield ValidationError(obj, msg, LABEL_ERROR)
+
+
+Validation.register_handler('odML', object_required_attributes)
+Validation.register_handler('section', object_required_attributes)
+Validation.register_handler('property', object_required_attributes)
+
+
 def section_type_must_be_defined(sec):
     """
     Tests that no Section has an undefined type.
@@ -282,6 +313,9 @@ def property_terminology_check(prop):
     2. warn, if there are multiple values with different units or the unit does
        not match the one in the terminology.
     """
+    if not prop.parent:
+        return
+
     tsec = prop.parent.get_terminology_equivalent()
     if tsec is None:
         return
@@ -300,6 +334,9 @@ def property_dependency_check(prop):
     Produces a warning if the dependency attribute refers to a non-existent attribute
     or the dependency_value does not match.
     """
+    if not prop.parent:
+        return
+
     dep = prop.dependency
     if dep is None:
         return
@@ -317,3 +354,35 @@ def property_dependency_check(prop):
 
 
 Validation.register_handler('property', property_dependency_check)
+
+
+def property_values_check(prop):
+    """
+    Tests that the values are of consistent dtype.
+    If dtype is not given, infer from first item in list.
+
+    :param prop: property the validation is applied on.
+    """
+
+    if prop.dtype is not None and prop.dtype != "":
+        dtype = prop.dtype
+    elif prop.values:
+        dtype = dtypes.infer_dtype(prop.values[0])
+    else:
+        return
+
+    for val in prop.values:
+        if dtype.endswith("-tuple"):
+            tuple_len = int(dtype[:-6])
+            if len(val) != tuple_len:
+                msg = "Tuple of length %s not consistent with dtype %s!" % (len(val), dtype)
+                yield ValidationError(prop, msg, LABEL_WARNING)
+        else:
+            try:
+                dtypes.get(val, dtype)
+            except ValueError:
+                msg = "Property values not of consistent dtype!"
+                yield ValidationError(prop, msg, LABEL_WARNING)
+
+
+Validation.register_handler('property', property_values_check)

test/test_doc_integration.py

@@ -104,25 +104,26 @@ def test_children(self):
         """
         This test checks the correct saving and loading of Section children of a Document.
         """
+        s_type = "type"
         # Lvl 1 child Sections
-        sec_lvl_11 = odml.Section(name="sec_11", parent=self.doc)
-        _ = odml.Section(name="sec_12", parent=self.doc)
+        sec_lvl_11 = odml.Section(name="sec_11", type=s_type, parent=self.doc)
+        _ = odml.Section(name="sec_12", type=s_type, parent=self.doc)
 
         # Lvl 2 child Sections
-        sec_lvl_21 = odml.Section(name="sec_21", parent=sec_lvl_11)
-        _ = odml.Section(name="sec_22", parent=sec_lvl_11)
-        _ = odml.Section(name="sec_23", parent=sec_lvl_11)
+        sec_lvl_21 = odml.Section(name="sec_21", type=s_type, parent=sec_lvl_11)
+        _ = odml.Section(name="sec_22", type=s_type, parent=sec_lvl_11)
+        _ = odml.Section(name="sec_23", type=s_type, parent=sec_lvl_11)
 
         # Lvl 2 child Properties
         _ = odml.Property(name="prop_21", parent=sec_lvl_11)
         _ = odml.Property(name="prop_22", parent=sec_lvl_11)
         _ = odml.Property(name="prop_23", parent=sec_lvl_11)
 
         # Lvl 3 child Sections
-        _ = odml.Section(name="sec_31", parent=sec_lvl_21)
-        _ = odml.Section(name="sec_32", parent=sec_lvl_21)
-        _ = odml.Section(name="sec_33", parent=sec_lvl_21)
-        _ = odml.Section(name="sec_34", parent=sec_lvl_21)
+        _ = odml.Section(name="sec_31", type=s_type, parent=sec_lvl_21)
+        _ = odml.Section(name="sec_32", type=s_type, parent=sec_lvl_21)
+        _ = odml.Section(name="sec_33", type=s_type, parent=sec_lvl_21)
+        _ = odml.Section(name="sec_34", type=s_type, parent=sec_lvl_21)
 
         # Lvl 3 child Properties
         _ = odml.Property(name="prop_31", parent=sec_lvl_21)

test/test_dumper.py

@@ -16,17 +16,19 @@ def setUp(self):
         self.captured_stdout = StringIO()
         sys.stdout = self.captured_stdout
 
+        s_type = "type"
+
         self.doc = odml.Document(author='Rave', version='1.0')
-        s1 = odml.Section(name='Cell')
+        s1 = odml.Section(name='Cell', type=s_type)
         p1 = odml.Property(name='Type', values='Rechargeable')
         s1.append(p1)
 
-        s2 = odml.Section(name='Electrolyte')
+        s2 = odml.Section(name='Electrolyte', type=s_type)
         p2 = odml.Property(name='Composition', values='Ni-Cd')
         s2.append(p2)
         s1.append(s2)
 
-        s3 = odml.Section(name='Electrode')
+        s3 = odml.Section(name='Electrode', type=s_type)
         p3 = odml.Property(name='Material', values='Nickel')
         p4 = odml.Property(name='Models', values=['AA', 'AAA'])
         s3.append(p3)
@@ -41,11 +43,11 @@ def test_dump_doc(self):
         odml.tools.dumper.dump_doc(self.doc)
         output = [x.strip() for x in self.captured_stdout.getvalue().split('\n') if x]
         expected_output = []
-        expected_output.append("*Cell ()")
+        expected_output.append("*Cell (type='type')")
         expected_output.append(":Type (values=Rechargeable, dtype='string')")
-        expected_output.append("*Electrolyte ()")
+        expected_output.append("*Electrolyte (type='type')")
         expected_output.append(":Composition (values=Ni-Cd, dtype='string')")
-        expected_output.append("*Electrode ()")
+        expected_output.append("*Electrode (type='type')")
         expected_output.append(":Material (values=Nickel, dtype='string')")
         expected_output.append(":Models (values=[AA,AAA], dtype='string')")
         self.assertEqual(len(output), len(expected_output))

test/test_section_integration.py

@@ -51,7 +51,8 @@ def save_load(self):
     def test_id(self):
         # Test correct save and load of generated id.
         sec_name = "empty_id"
-        sec = odml.Section(name=sec_name, parent=self.doc)
+        sec_type = "type"
+        sec = odml.Section(name=sec_name, type=sec_type, parent=self.doc)
 
         jdoc, xdoc, ydoc = self.save_load()
 
@@ -62,7 +63,7 @@ def test_id(self):
         # Test correct save and load of assigned id.
         sec_name = "assigned_id"
         assigned_id = "79b613eb-a256-46bf-84f6-207df465b8f7"
-        _ = odml.Section(name=sec_name, oid=assigned_id, parent=self.doc)
+        _ = odml.Section(name=sec_name, oid=assigned_id, type=sec_type, parent=self.doc)
 
         jdoc, xdoc, ydoc = self.save_load()
 
@@ -116,31 +117,32 @@ def test_children(self):
         This test checks correct writing and loading of Section and Property
         children of a Section.
         """
-        root = odml.Section(name="root", parent=self.doc)
+        s_type = "type"
+        root = odml.Section(name="root", type=s_type, parent=self.doc)
 
         # Lvl 1 child Sections
-        sec_lvl_11 = odml.Section(name="sec_11", parent=root)
-        _ = odml.Section(name="sec_12", parent=root)
+        sec_lvl_11 = odml.Section(name="sec_11", type=s_type, parent=root)
+        _ = odml.Section(name="sec_12", type=s_type, parent=root)
 
         # Lvl 1 child Properties
         _ = odml.Property(name="prop_11", parent=root)
         _ = odml.Property(name="prop_12", parent=root)
 
         # Lvl 2 child Sections
-        sec_lvl_21 = odml.Section(name="sec_21", parent=sec_lvl_11)
-        _ = odml.Section(name="sec_22", parent=sec_lvl_11)
-        _ = odml.Section(name="sec_23", parent=sec_lvl_11)
+        sec_lvl_21 = odml.Section(name="sec_21", type=s_type, parent=sec_lvl_11)
+        _ = odml.Section(name="sec_22", type=s_type, parent=sec_lvl_11)
+        _ = odml.Section(name="sec_23", type=s_type, parent=sec_lvl_11)
 
         # Lvl 2 child Properties
         _ = odml.Property(name="prop_21", parent=sec_lvl_11)
         _ = odml.Property(name="prop_22", parent=sec_lvl_11)
         _ = odml.Property(name="prop_23", parent=sec_lvl_11)
 
         # Lvl 3 child Sections
-        _ = odml.Section(name="sec_31", parent=sec_lvl_21)
-        _ = odml.Section(name="sec_32", parent=sec_lvl_21)
-        _ = odml.Section(name="sec_33", parent=sec_lvl_21)
-        _ = odml.Section(name="sec_34", parent=sec_lvl_21)
+        _ = odml.Section(name="sec_31", type=s_type, parent=sec_lvl_21)
+        _ = odml.Section(name="sec_32", type=s_type, parent=sec_lvl_21)
+        _ = odml.Section(name="sec_33", type=s_type, parent=sec_lvl_21)
+        _ = odml.Section(name="sec_34", type=s_type, parent=sec_lvl_21)
 
         # Lvl 3 child Properties
         _ = odml.Property(name="prop_31", parent=sec_lvl_21)

test/test_validation.py

@@ -126,3 +126,29 @@ def test_section_unique_ids(self):
 
         res = validate(doc)
         self.assertError(res, "Duplicate id in Section")
+
+    def test_standalone_section(self):
+        """
+        Test if standalone section does not return errors if required attributes are correct.
+        If type is undefined, check error message.
+        """
+
+        sec_one = odml.Section("sec1")
+
+        res = validate(sec_one)
+        self.assertError(res, "Section type undefined")
+
+        doc = samplefile.parse("""s1[undefined]""")
+        res = validate(doc)
+        self.assertError(res, "Section type undefined")
+
+    def test_standalone_property(self):
+        """
+        Test if standalone property does not return errors if required attributes are correct.
+        """
+
+        prop = odml.Property()
+        prop.type = ""
+
+        for err in validate(prop).errors:
+            assert not err.is_error