Merge pull request #321 from fschrader1992/master

Automatically Add IDs At Verison Conversion

Author: mpsonntag

odml/doc.py

@@ -141,3 +141,21 @@ def get_terminology_equivalent(self):
             return None
         term = terminology.load(self.repository)
         return term
+def pprint(self, indent=2, max_depth=1, max_length=80, current_depth=0):
+    """
+    Pretty print method to visualize Document-Section trees.
+
+    :param indent: number of leading spaces for every child Section or Property.
+    :param max_depth: maximum number of hierarchical levels printed from the
+                          starting Section.
+    :param max_length: maximum number of characters printed in one line.
+    :param current_depth: number of hierarchical levels printed from the
+                          starting Section.
+    """
+    doc_str = "[{} [{}] {}, sections: {}, repository: {}]".format(self.author, self.version,
+                                                                  self.date, len(self._sections), self.repository)
+    print(doc_str)
+
+    for s in self._sections:
+        s.pprint(current_depth=current_depth+1, max_depth=max_depth,
+                 indent=indent, max_length=max_length)

odml/dtypes.py

@@ -62,6 +62,8 @@ def default_values(dtype):
 
 _dtype_map = {'str': 'string', 'bool': 'boolean'}
 
+special_dtypes = ["url", "person", "text"]
+
 
 def infer_dtype(value):
     dtype = (type(value)).__name__

odml/property.py

@@ -82,7 +82,7 @@ def __init__(self, name=None, values=None, parent=None, unit=None,
 
         self._values = []
         self.values = values
-        if not values and (value or isinstance(value, bool)):
+        if not values and (value or isinstance(value, bool) or isinstance(value, int)):
             self.values = value
 
         self.parent = parent
@@ -588,8 +588,10 @@ def extend(self, obj, strict=True):
 
         new_value = self._convert_value_input(obj)
         if len(new_value) > 0 and strict and dtypes.infer_dtype(new_value[0]) != self.dtype:
-            raise ValueError("odml.Property.extend: "
-                             "passed value data type does not match dtype!")
+
+            if not (dtypes.infer_dtype(new_value[0]) == "string" and self.dtype in dtypes.special_dtypes):
+                raise ValueError("odml.Property.extend: passed value data type found (\"%s\") "
+                                 "does not match expected dtype \"%s\"!" % (dtypes.infer_dtype(new_value[0]), self._dtype))
 
         if not self._validate_values(new_value):
             raise ValueError("odml.Property.extend: passed value(s) cannot be converted "
@@ -618,8 +620,10 @@ def append(self, obj, strict=True):
             raise ValueError("odml.property.append: Use extend to add a list of values!")
 
         if len(new_value) > 0 and strict and dtypes.infer_dtype(new_value[0]) != self.dtype:
-            raise ValueError("odml.Property.append: "
-                             "passed value data type does not match dtype!")
+
+            if not (dtypes.infer_dtype(new_value[0]) == "string" and self.dtype in dtypes.special_dtypes):
+                raise ValueError("odml.Property.append: passed value data type found (\"%s\") "
+                                 "does not match expected dtype \"%s\"!" % (dtypes.infer_dtype(new_value[0]), self._dtype))
 
         if not self._validate_values(new_value):
             raise ValueError("odml.Property.append: passed value(s) cannot be converted "

odml/tools/version_converter.py

@@ -9,6 +9,8 @@
 from ..info import FORMAT_VERSION
 from ..terminology import Terminologies, REPOSITORY_BASE
 
+import uuid
+
 try:
     unicode = unicode
 except NameError:
@@ -194,6 +196,8 @@ def _convert(self, tree):
             if e.tag == "repository":
                 self._handle_repository(e)
 
+        tree = self._check_add_ids(tree)
+
         return tree
 
     def _handle_include(self, element):
@@ -410,6 +414,41 @@ def _change_entity_name(tree, elem_map, name):
             elem_map[named_path] += 1
             name.text += "-" + str(elem_map[named_path])
 
+    def _check_add_ids(self, tree):
+        """
+        Checks, whether elements (properties) possess an UUID
+        and adds one in case of absence.
+        :param tree: ElementTree of the doc
+        :return: ElementTree
+        """
+        root = tree.getroot()
+        self._add_id(root)
+        for sec in root.iter("section"):
+            self._add_id(sec)
+            for prop in sec.iter("property"):
+                self._add_id(prop)
+
+        return tree
+
+    @staticmethod
+    def _add_id(element):
+        """
+        Checks, whether an element possesses an ID. If yes, make sure it has
+        the right format. Otherwise a new UUID is created.
+        :param element: lxml element.
+        """
+        oid = element.find("id")
+        new_id = ET.Element("id")
+        new_id.text = str(uuid.uuid4())
+        if oid is not None:
+            try:
+                if oid.text is not None:
+                    new_id.text = str(uuid.UUID(oid.text))
+            except ValueError as e:
+                print(e)
+            element.remove(oid)
+        element.append(new_id)
+
     def _log(self, msg):
         """
         Adds the passed message to the conversion_log attribute and

test/test_property.py

@@ -103,6 +103,18 @@ def test_value(self):
         with self.assertRaises(ValueError):
             _ = Property(name="Public-Key", value='(5689; 1254; 687)', dtype='2-tuple')
 
+        p3 = Property('myprop', value=0, dtype=DType.int)
+        self.assertEqual(p3.value, [0])
+        self.assertEqual(p3.values, [0])
+
+        p4 = Property('myprop', value=0, dtype=DType.boolean)
+        self.assertEqual(p4.value, [False])
+        self.assertEqual(p4.values, [False])
+
+        p5 = Property('myprop', value=0)
+        self.assertEqual(p5.value, [0])
+        self.assertEqual(p5.values, [0])
+
     def test_value_append(self):
         # Test append w/o Property value or dtype
         prop = Property(name="append")
@@ -183,6 +195,27 @@ def test_value_append(self):
         self.assertEqual(len(p5), 2)
         self.assertRaises(ValueError, p5.append, "[a, b, c]")
 
+        p6 = Property(name="prop", value=["A Abraham", "B Barnes", "C Clark"], dtype=DType.person)
+        p6.append("D Dickins")
+        self.assertEqual(len(p6), 4)
+        self.assertRaises(ValueError, p6.append, 1)
+        self.assertRaises(ValueError, p6.append, 1.3)
+        self.assertRaises(ValueError, p6.append, True)
+
+        p7 = Property(name="prop", value=["https://en.wikipedia.org/wiki/Earth"], dtype=DType.url)
+        p7.append("https://en.wikipedia.org/wiki/Mars")
+        self.assertEqual(len(p7), 2)
+        self.assertRaises(ValueError, p7.append, 1)
+        self.assertRaises(ValueError, p7.append, 1.3)
+        self.assertRaises(ValueError, p7.append, True)
+
+        p8 = Property(name="prop", value=["Earth is No. 3."], dtype=DType.text)
+        p8.append("Mars is No. 4.")
+        self.assertEqual(len(p8), 2)
+        self.assertRaises(ValueError, p8.append, 1)
+        self.assertRaises(ValueError, p8.append, 1.3)
+        self.assertRaises(ValueError, p8.append, True)
+
     def test_value_extend(self):
         prop = Property(name="extend")
 
@@ -260,6 +293,27 @@ def test_value_extend(self):
         with self.assertRaises(ValueError):
             prop.extend([6, "some text"])
 
+        p1 = Property(name="prop", value=["A Abraham", "B Barnes", "C Clark"], dtype=DType.person)
+        p1.extend("D Dickins")
+        self.assertEqual(len(p1), 4)
+        self.assertRaises(ValueError, p1.extend, 1)
+        self.assertRaises(ValueError, p1.extend, 1.3)
+        self.assertRaises(ValueError, p1.extend, True)
+
+        p2 = Property(name="prop", value=["https://en.wikipedia.org/wiki/Earth"], dtype=DType.url)
+        p2.extend("https://en.wikipedia.org/wiki/Mars")
+        self.assertEqual(len(p2), 2)
+        self.assertRaises(ValueError, p2.append, 1)
+        self.assertRaises(ValueError, p2.append, 1.3)
+        self.assertRaises(ValueError, p2.append, True)
+
+        p3 = Property(name="prop", value=["Earth is No. 3."], dtype=DType.text)
+        p3.extend("Mars is No. 4.")
+        self.assertEqual(len(p3), 2)
+        self.assertRaises(ValueError, p3.append, 1)
+        self.assertRaises(ValueError, p3.append, 1.3)
+        self.assertRaises(ValueError, p3.append, True)
+
     def test_get_set_value(self):
         values = [1, 2, 3, 4, 5]
         p = Property("property", value=values)