Merge pull request #385 from mpsonntag/cleanUpdate

General updates and PEP8 code cleanup

Author: jgrewe

README.md

@@ -1,6 +1,6 @@
-![Travis build](https://travis-ci.org/G-Node/python-odml.svg?branch=master)
+[![Travis build](https://travis-ci.org/G-Node/python-odml.svg?branch=master)](https://travis-ci.org/G-Node/python-odml)
 [![Build status](https://ci.appveyor.com/api/projects/status/br7pe6atlwdg5618/branch/master?svg=true)](https://ci.appveyor.com/project/G-Node/python-odml/branch/master)
-![Test coverage](https://coveralls.io/repos/github/G-Node/python-odml/badge.svg?branch=master)
+[![Test coverage](https://coveralls.io/repos/github/G-Node/python-odml/badge.svg?branch=master)](https://coveralls.io/github/G-Node/python-odml)
 [![PyPI version](https://img.shields.io/pypi/v/odml.svg)](https://pypi.org/project/odML/)
 [![Read the Docs](https://img.shields.io/readthedocs/python-odml)](https://python-odml.readthedocs.io/en/latest/)
 

doc/tutorial.rst

@@ -70,8 +70,9 @@ experimental project and complements the special needs of your laboratory.
 The code for the example odML files, which we use within this tutorial is part
 of the documentation package (see doc/example_odMLs/).
 
-A summary of available odML terminologies and templates can be found `here
-<https://terminologies.g-node.org/v1.1/terminologies.xml>`_.
+A summary of available odML terminologies and templates can be found at the G-Node `odML terminology
+<https://terminologies.g-node.org/v1.1/terminologies.xml>`_ and `odML template
+<https://templates.g-node.org/>`_ pages.
 
 -------------------------------------------------------------------------------
 
@@ -311,7 +312,6 @@ following command::
 As expected from the Document printout our example contains two Sections. The
 printout and attributes of a Section are explained in the next chapter.
 
-
 The Sections
 ------------
 
@@ -553,6 +553,18 @@ returned list will have no affect on the actual Property values. If you want to
 make changes to a Property value, either use the ``append``, ``extend`` and ``remove``
 methods or assign a new value list to the property.
 
+Printing overviews to navigate the contents of an odML document
+---------------------------------------------------------------
+
+The odML entities ``Property``, ``Section`` and ``Document`` feature
+a method that allows to print a tree-like representation of
+all child entities to get an overview of the file structure.
+
+    >>> MYodML.pprint()
+    >>> sec = MYodML['TheCrew']
+    >>> sec.pprint()
+    >>> prop = odmlEX['TheCrew'].properties['NameCrewMembers']
+    >>> prop.pprint()
 
 -------------------------------------------------------------------------------
 
@@ -930,6 +942,48 @@ Also note that any style that is saved with an odML document will be lost, when
 document is loaded again and changes to the content are added. In this case the required
 style needs to be specified again when saving the changed file as described above.
 
+
+Defining and working with feature cardinality
+---------------------------------------------
+
+The odML format allows users to define a cardinality for
+the number of subsections and properties of Sections and
+the number of values a Property might have.
+
+A cardinality is checked when it is set, when its target is
+set and when a document is saved or loaded. If a specific
+cardinality is violated, a corresponding warning will be printed.
+
+Setting a cardinality
+*********************
+
+A cardinality can be set for sections or properties of sections
+or for values of properties. By default every cardinality is None,
+but it can be set to a defined minimal and/or a maximal number of
+an element.
+
+A cardinality is set via its convenience method:
+
+    >>> # Set the cardinality of the properties of a Section 'sec' to
+    >>> # a maximum of 5 elements.
+    >>> sec = odml.Section(name="cardinality", type="test")
+    >>> sec.set_properties_cardinality(max_val=5)
+
+    >>> # Set the cardinality of the subsections of Section 'sec' to
+    >>> # a minimum of one and a maximum of 2 elements.
+    >>> sec.set_sections_cardinality(min_val=1, max_val=2)
+
+    >>> # Set the cardinality of the values of a Property 'prop' to
+    >>> # a minimum of 1 element.
+    >>> prop = odml.Property(name="cardinality")
+    >>> prop.set_values_cardinality(min_val=1)
+
+    >>> # Re-set the cardinality of the values of a Property 'prop' to not set.
+    >>> prop.set_values_cardinality()
+    >>> # or
+    >>> prop.val_cardinality = None
+
+
 Advanced knowledge on Values
 ----------------------------
 

odml/base.py

@@ -2,6 +2,7 @@
 """
 This module provides base classes for functionality common to odML objects.
 """
+import copy
 import posixpath
 
 try:
@@ -36,9 +37,10 @@ def __eq__(self, obj):
             return False
 
         for key in self._format:
-            if key == "id" or key == "oid":
+            if key in ["id", "oid"]:
                 continue
-            elif getattr(self, key) != getattr(obj, key):
+
+            if getattr(self, key) != getattr(obj, key):
                 return False
 
         return True
@@ -87,7 +89,6 @@ def clone(self, children=True):
                          from this class.
         """
         # TODO don't we need some recursion / deepcopy here?
-        import copy
         obj = copy.copy(self)
         return obj
 
@@ -149,6 +150,8 @@ def __contains__(self, key):
             if (hasattr(obj, "name") and obj.name == key) or key == obj:
                 return True
 
+        return False
+
     def __eq__(self, obj):
         """
         SmartList attributes of 'sections' and 'properties' are
@@ -292,7 +295,7 @@ def extend(self, sec_list):
             if not isinstance(sec, BaseSection):
                 raise ValueError("Can only extend objects of type Section.")
 
-            elif isinstance(sec, BaseSection) and sec.name in self._sections:
+            if isinstance(sec, BaseSection) and sec.name in self._sections:
                 raise KeyError("Section with name '%s' already exists." % sec.name)
 
         for sec in sec_list:
@@ -356,9 +359,9 @@ def iterproperties(self, max_depth=None, filter_func=lambda x: True):
                             iterable. Yields iterable if function returns True
         :type filter_func: function
         """
-        for sec in [s for s in self.itersections(max_depth=max_depth,
-                                                 yield_self=True)]:
-            if hasattr(sec, "properties"):  # not to fail if odml.Document
+        for sec in list(self.itersections(max_depth=max_depth, yield_self=True)):
+            # Avoid fail with an odml.Document
+            if hasattr(sec, "properties"):
                 for i in sec.properties:
                     if filter_func(i):
                         yield i
@@ -380,7 +383,7 @@ def itervalues(self, max_depth=None, filter_func=lambda x: True):
                             iterable. Yields iterable if function returns True
         :type filter_func: function
         """
-        for prop in [p for p in self.iterproperties(max_depth=max_depth)]:
+        for prop in list(self.iterproperties(max_depth=max_depth)):
             if filter_func(prop.values):
                 yield prop.values
 
@@ -478,9 +481,10 @@ def _get_section_by_path(self, path):
 
             if found:
                 return found._get_section_by_path("/".join(pathlist[1:]))
+
             raise ValueError("Section named '%s' does not exist" % pathlist[0])
-        else:
-            return self._match_iterable(self.sections, pathlist[0])
+
+        return self._match_iterable(self.sections, pathlist[0])
 
     def find(self, key=None, type=None, findAll=False, include_subtype=False):
         """

odml/doc.py

@@ -122,6 +122,20 @@ def parent(self):
         """ The parent of a document is always None. """
         return None
 
+    @property
+    def origin_file_name(self):
+        """
+        If available, the file name from where the document has been loaded.
+        Will not be serialized to file when saving the document.
+        """
+        return self._origin_file_name
+
+    @origin_file_name.setter
+    def origin_file_name(self, new_value):
+        if not new_value:
+            new_value = None
+        self._origin_file_name = new_value
+
     def finalize(self):
         """
         This needs to be called after the document is set up from parsing

odml/property.py

@@ -253,7 +253,8 @@ def parent(self):
     def parent(self, new_parent):
         if new_parent is None and self._parent is None:
             return
-        elif new_parent is None and self._parent is not None:
+
+        if new_parent is None and self._parent is not None:
             self._parent.remove(self)
             self._parent = None
         elif self._validate_parent(new_parent):
@@ -319,7 +320,8 @@ def _validate_values(self, values):
                 return False
         return True
 
-    def _convert_value_input(self, new_value):
+    @staticmethod
+    def _convert_value_input(new_value):
         """
         This method ensures, that the passed new value is a list.
         If new_value is a string, it will convert it to a list of
@@ -403,14 +405,12 @@ def values(self, new_value):
             new_value = odml_tuple_import(t_count, new_value)
 
         if not self._validate_values(new_value):
+            msg = "odml.Property.values: passed values are not of consistent type"
             if self._dtype in ("date", "time", "datetime"):
                 req_format = dtypes.default_values(self._dtype)
-                msg = "odml.Property.values: passed values are not of consistent type "
-                msg += "\'%s\'! Format should be \'%s\'." % (self._dtype, req_format)
-                raise ValueError(msg)
-            else:
-                msg = "odml.Property.values: passed values are not of consistent type!"
-                raise ValueError(msg)
+                msg += " \'%s\'! Format should be \'%s\'." % (self._dtype, req_format)
+            raise ValueError(msg)
+
         self._values = [dtypes.get(v, self.dtype) for v in new_value]
 
         # Validate and inform user if the current values cardinality is violated
@@ -714,10 +714,10 @@ def get_merged_equivalent(self):
         Return the merged object (i.e. if the parent section is linked to another one,
         return the corresponding property of the linked section) or None.
         """
-        if self.parent is None or self.parent._merged is None:
+        if self.parent is None or not self.parent.is_merged:
             return None
 
-        return self.parent._merged.contains(self)
+        return self.parent.get_merged_equivalent().contains(self)
 
     @inherit_docstring
     def get_terminology_equivalent(self):
@@ -841,26 +841,16 @@ def pprint(self, indent=2, max_length=80, current_depth=-1):
 
     def export_leaf(self):
         """
-        Export only the path from this property to the root.
-        Include all properties of parent sections.
-
-        :returns: cloned odml tree to the root of the current document.
-        """
-        curr = self.parent
-        par = self.parent
-        child = self.parent
-
-        while curr is not None:
-            par = curr.clone(children=False, keep_id=True)
-            if curr != self.parent:
-                par.append(child)
-            if hasattr(curr, 'properties'):
-                if curr == self.parent:
-                    par.append(self.clone(keep_id=True))
-                else:
-                    for prop in curr.properties:
-                        par.append(prop.clone(keep_id=True))
-            child = par
-            curr = curr.parent
-
-        return par
+        Export the path including all direct parents from this Property
+        to the root of the document. Section properties are included,
+        Subsections are not included.
+
+        :returns: Cloned odml tree to the root of the current document.
+        """
+        export = self
+        if export.parent:
+            # Section.export_leaf will take care of the full export and
+            # include the current Property.
+            export = export.parent.export_leaf()
+
+        return export

odml/section.py

@@ -54,7 +54,6 @@ class BaseSection(base.Sectionable):
     """
 
     type = None
-    reference = None  # the *import* property
     _link = None
     _include = None
     _merged = None
@@ -328,7 +327,8 @@ def parent(self):
     def parent(self, new_parent):
         if new_parent is None and self._parent is None:
             return
-        elif new_parent is None and self._parent is not None:
+
+        if new_parent is None and self._parent is not None:
             self._parent.remove(self)
             self._parent = None
         elif self._validate_parent(new_parent):
@@ -341,7 +341,8 @@ def parent(self, new_parent):
                 "odml.Section.parent: passed value is not of consistent type!"
                 "\nodml.Document or odml.Section expected")
 
-    def _validate_parent(self, new_parent):
+    @staticmethod
+    def _validate_parent(new_parent):
         """
         Checks whether a provided object is a valid odml.Section or odml.Document..
 
@@ -402,9 +403,9 @@ def set_sections_cardinality(self, min_val=None, max_val=None):
         Sets the Sections cardinality of a Section.
 
         :param min_val: Required minimal number of values elements. None denotes
-                        no restrictions on values elements minimum. Default is None.
+                        no restrictions on sections elements minimum. Default is None.
         :param max_val: Allowed maximal number of values elements. None denotes
-                        no restrictions on values elements maximum. Default is None.
+                        no restrictions on sections elements maximum. Default is None.
         """
         self.sec_cardinality = (min_val, max_val)
 
@@ -455,9 +456,9 @@ def set_properties_cardinality(self, min_val=None, max_val=None):
         Sets the Properties cardinality of a Section.
 
         :param min_val: Required minimal number of values elements. None denotes
-                        no restrictions on values elements minimum. Default is None.
+                        no restrictions on properties elements minimum. Default is None.
         :param max_val: Allowed maximal number of values elements. None denotes
-                        no restrictions on values elements maximum. Default is None.
+                        no restrictions on properties elements maximum. Default is None.
         """
         self.prop_cardinality = (min_val, max_val)
 
@@ -521,16 +522,16 @@ def extend(self, obj_list):
         # Make sure only Sections and Properties with unique names will be added.
         for obj in obj_list:
             if not isinstance(obj, BaseSection) and not isinstance(obj, BaseProperty):
-                raise ValueError("odml.Section.extend: "
-                                 "Can only extend sections and properties.")
+                msg = "odml.Section.extend: Can only extend sections and properties."
+                raise ValueError(msg)
 
-            elif isinstance(obj, BaseSection) and obj.name in self.sections:
-                raise KeyError("odml.Section.extend: "
-                               "Section with name '%s' already exists." % obj.name)
+            if isinstance(obj, BaseSection) and obj.name in self.sections:
+                msg = "odml.Section.extend: Section with name '%s' already exists." % obj.name
+                raise KeyError(msg)
 
-            elif isinstance(obj, BaseProperty) and obj.name in self.properties:
-                raise KeyError("odml.Section.extend: "
-                               "Property with name '%s' already exists." % obj.name)
+            if isinstance(obj, BaseProperty) and obj.name in self.properties:
+                msg = "odml.Section.extend: Property with name '%s' already exists." % obj.name
+                raise KeyError(msg)
 
         for obj in obj_list:
             self.append(obj)
@@ -613,13 +614,14 @@ def contains(self, obj):
         if isinstance(obj, BaseSection):
             return super(BaseSection, self).contains(obj)
 
-        elif isinstance(obj, BaseProperty):
+        if isinstance(obj, BaseProperty):
             for i in self._props:
                 if obj.name == i.name:
                     return i
-        else:
-            raise ValueError("odml.Section.contains:"
-                             "Section or Property object expected.")
+
+            return None
+
+        raise ValueError("odml.Section.contains: Section or Property object expected.")
 
     def merge_check(self, source_section, strict=True):
         """

odml/tools/converters/format_converter.py

@@ -79,7 +79,7 @@ def convert(cls, args=None):
         parser.add_argument("-r", "--recursive", action="store_true",
                             help="Enable converting files from subdirectories")
         args = parser.parse_args(args)
-        recursive = True if args.recursive else False
+        recursive = bool(args.recursive)
         cls.convert_dir(args.input_dir, args.output_dir, recursive, args.result_format)
 
     @classmethod