Merge pull request #287 from mpsonntag/idRename

[1.4] 'id' attribute renaming and small fixes

LGTM

Author: achilleas-k

doc/example_odMLs/ex_2.odml

@@ -29,7 +29,7 @@ def __eq__(self, obj):
             return False
 
         for key in self._format:
-            if key == "id":
+            if key == "id" or key == "oid":
                 continue
             elif getattr(self, key) != getattr(obj, key):
                 return False

doc/example_odMLs/odml_ex_1_generator.py

@@ -19,11 +19,11 @@ class BaseDocument(base.Sectionable):
 
     _format = format.Document
 
-    def __init__(self, author=None, date=None, version=None, repository=None, id=None):
+    def __init__(self, author=None, date=None, version=None, repository=None, oid=None):
         super(BaseDocument, self).__init__()
         try:
-            if id is not None:
-                self._id = str(uuid.UUID(id))
+            if oid is not None:
+                self._id = str(uuid.UUID(oid))
             else:
                 self._id = str(uuid.uuid4())
         except ValueError as e:
@@ -41,22 +41,30 @@ def __repr__(self):
         return "<Doc %s by %s (%d sections)>" % (self._version, self._author,
                                                  len(self._sections))
 
+    @property
+    def oid(self):
+        """
+        The uuid for the document. Required for entity creation and comparison,
+        saving and loading.
+        """
+        return self.id
+
     @property
     def id(self):
         """
         The uuid for the document.
         """
         return self._id
 
-    def new_id(self, id=None):
+    def new_id(self, oid=None):
         """
         new_id sets the id of the current object to a RFC 4122 compliant UUID.
         If an id was provided, it is assigned if it is RFC 4122 UUID format compliant.
         If no id was provided, a new UUID is generated and assigned.
-        :param id: UUID string as specified in RFC 4122.
+        :param oid: UUID string as specified in RFC 4122.
         """
-        if id is not None:
-            self._id = str(uuid.UUID(id))
+        if oid is not None:
+            self._id = str(uuid.UUID(oid))
         else:
             self._id = str(uuid.uuid4())
 

doc/example_odMLs/ex_1.odml doc/example_odMLs/sample_odml.odmldoc/example_odMLs/ex_1.odml renamed to doc/example_odMLs/sample_odml.odml

@@ -108,7 +108,8 @@ class Property(Format):
     }
     _map = {
         'dependencyvalue': 'dependency_value',
-        'type': 'dtype'
+        'type': 'dtype',
+        'id': 'oid'
     }
     _rdf_map = {
         'id': _ns.hasId,
@@ -142,6 +143,7 @@ class Section(Format):
     _map = {
         'section': 'sections',
         'property': 'properties',
+        'id': 'oid'
     }
     _rdf_map = {
         'id': _ns.hasId,
@@ -168,7 +170,8 @@ class Document(Format):
         'repository': 0,
     }
     _map = {
-        'section': 'sections'
+        'section': 'sections',
+        'id': 'oid'
     }
     _rdf_map = {
         'id': _ns.hasId,

doc/example_odMLs/ex_1.rdf doc/example_odMLs/sample_odml.rdfdoc/example_odMLs/ex_1.rdf renamed to doc/example_odMLs/sample_odml.rdf

@@ -16,7 +16,7 @@ class BaseProperty(base.BaseObject):
     def __init__(self, name=None, value=None, parent=None, unit=None,
                  uncertainty=None, reference=None, definition=None,
                  dependency=None, dependency_value=None, dtype=None,
-                 value_origin=None, id=None):
+                 value_origin=None, oid=None):
         """
         Create a new Property. If a value without an explicitly stated dtype
         has been provided, the method will try to infer the value's dtype.
@@ -45,13 +45,13 @@ def __init__(self, name=None, value=None, parent=None, unit=None,
                       if dtype is not given, the type is deduced from the values.
                       Check odml.DType for supported data types.
         :param value_origin: Reference where the value originated from e.g. a file name.
-        :param id: UUID string as specified in RFC 4122. If no id is provided,
+        :param oid: object id, UUID string as specified in RFC 4122. If no id is provided,
                    an id will be generated and assigned. An id has to be unique
                    within an odML Document.
         """
         try:
-            if id is not None:
-                self._id = str(uuid.UUID(id))
+            if oid is not None:
+                self._id = str(uuid.UUID(oid))
             else:
                 self._id = str(uuid.uuid4())
         except ValueError as e:
@@ -101,19 +101,30 @@ def __setitem__(self, key, item):
             raise ValueError("odml.Property.__setitem__:  passed value cannot be "
                              "converted to data type \'%s\'!" % self._dtype)
 
+    @property
+    def oid(self):
+        """
+        The uuid for the property. Required for entity creation and comparison,
+        saving and loading.
+        """
+        return self.id
+
     @property
     def id(self):
+        """
+        The uuid for the property.
+        """
         return self._id
 
-    def new_id(self, id=None):
+    def new_id(self, oid=None):
         """
-        new_id sets the id of the current object to an RFC 4122 compliant UUID.
+        new_id sets the object id of the current object to an RFC 4122 compliant UUID.
         If an id was provided, it is assigned if it is RFC 4122 UUID format compliant.
         If no id was provided, a new UUID is generated and assigned.
-        :param id: UUID string as specified in RFC 4122.
+        :param oid: UUID string as specified in RFC 4122.
         """
-        if id is not None:
-            self._id = str(uuid.UUID(id))
+        if oid is not None:
+            self._id = str(uuid.UUID(oid))
         else:
             self._id = str(uuid.uuid4())
 

odml/base.py

@@ -16,26 +16,24 @@
 class BaseSection(base.Sectionable):
     """ An odML Section """
     type = None
-    # id = None
+    reference = None  # the *import* property
     _link = None
     _include = None
-    reference = None  # the *import* property
-
     _merged = None
 
     _format = format.Section
 
     def __init__(self, name=None, type=None, parent=None,
                  definition=None, reference=None,
-                 repository=None, link=None, include=None, id=None):
+                 repository=None, link=None, include=None, oid=None):
 
         # Sets _sections Smartlist and _repository to None, so run first.
         super(BaseSection, self).__init__()
         self._props = base.SmartList(BaseProperty)
 
         try:
-            if id is not None:
-                self._id = str(uuid.UUID(id))
+            if oid is not None:
+                self._id = str(uuid.UUID(oid))
             else:
                 self._id = str(uuid.uuid4())
         except ValueError as e:
@@ -76,19 +74,30 @@ def __len__(self):
         """
         return len(self._sections) + len(self._props)
 
+    @property
+    def oid(self):
+        """
+        The uuid for the section. Required for entity creation and comparison,
+        saving and loading.
+        """
+        return self.id
+
     @property
     def id(self):
+        """
+        The uuid for the section.
+        """
         return self._id
 
-    def new_id(self, id=None):
+    def new_id(self, oid=None):
         """
         new_id sets the id of the current object to a RFC 4122 compliant UUID.
         If an id was provided, it is assigned if it is RFC 4122 UUID format compliant.
         If no id was provided, a new UUID is generated and assigned.
-        :param id: UUID string as specified in RFC 4122.
+        :param oid: UUID string as specified in RFC 4122.
         """
-        if id is not None:
-            self._id = str(uuid.UUID(id))
+        if oid is not None:
+            self._id = str(uuid.UUID(oid))
         else:
             self._id = str(uuid.uuid4())
 

odml/doc.py

@@ -33,7 +33,8 @@ def to_dict(self, odml_document):
                     tag = getattr(odml_document, attr)
 
                     if tag:
-                        parsed_doc[attr] = tag
+                        # Always use the arguments key attribute name when saving
+                        parsed_doc[i] = tag
 
         return parsed_doc
 
@@ -60,7 +61,8 @@ def get_sections(self, section_list):
                         tag = getattr(section, attr)
 
                         if tag:
-                            section_dict[attr] = tag
+                            # Always use the arguments key attribute name when saving
+                            section_dict[i] = tag
 
             section_seq.append(section_dict)
 
@@ -89,7 +91,8 @@ def get_properties(props_list):
                                 prop.dtype.endswith("-tuple") and len(prop.value) > 0:
                             prop_dict["value"] = "(%s)" % ";".join(prop.value[0])
                         else:
-                            prop_dict[attr] = tag
+                            # Always use the arguments key attribute name when saving
+                            prop_dict[i] = tag
 
             props_seq.append(prop_dict)
 
@@ -128,9 +131,9 @@ def to_odml(self, parsed_doc):
             raise ParserException("Invalid odML document: Could not find odml-version.")
 
         elif self.parsed_doc.get('odml-version') != FORMAT_VERSION:
-            msg = ("Cannot read file: invalid odML document format version '%s'. \n"
-                   "This package supports odML format versions: '%s'."
-                   % (self.parsed_doc.get('odml-version'), FORMAT_VERSION))
+            msg = ("Cannot parse odML document with format version '%s'. \n"
+                   "\tUse the 'tools.VersionConverter' to import previous odML formats."
+                   % self.parsed_doc.get('odml-version'))
             raise InvalidVersionException(msg)
 
         self.parsed_doc = self.parsed_doc['Document']
@@ -143,7 +146,8 @@ def to_odml(self, parsed_doc):
             if attr == 'sections':
                 doc_secs = self.parse_sections(self.parsed_doc['sections'])
             elif attr:
-                doc_attrs[i] = self.parsed_doc[i]
+                # Make sure to always use the correct odml format attribute name
+                doc_attrs[odmlfmt.Document.map(attr)] = self.parsed_doc[i]
 
         doc = odmlfmt.Document.create(**doc_attrs)
         for sec in doc_secs:
@@ -166,7 +170,8 @@ def parse_sections(self, section_list):
                 elif attr == 'sections':
                     children_secs = self.parse_sections(section['sections'])
                 elif attr:
-                    sec_attrs[attr] = section[attr]
+                    # Make sure to always use the correct odml format attribute name
+                    sec_attrs[odmlfmt.Section.map(attr)] = section[attr]
 
             sec = odmlfmt.Section.create(**sec_attrs)
             for prop in sec_props:
@@ -188,7 +193,8 @@ def parse_properties(self, props_list):
             for i in _property:
                 attr = self.is_valid_attribute(i, odmlfmt.Property)
                 if attr:
-                    prop_attrs[attr] = _property[attr]
+                    # Make sure to always use the correct odml format attribute name
+                    prop_attrs[odmlfmt.Property.map(attr)] = _property[attr]
 
             prop = odmlfmt.Property.create(**prop_attrs)
             odml_props.append(prop)