Cleanup: Use file references whenever appropriate

- Removed hacky parent traversal for getting root objects like the top
  level metadata container.
- Removed H5Group utility functions that are now obsolete.
- Containers that need to do a search from the root object to delete
  objects now use the file reference.

Author: achilleas-k

nixio/container.py

@@ -57,10 +57,7 @@ def __delitem__(self, item):
                     self._itemclass.__name__)
             )
 
-        root = self._backend.h5root
-        if not root:
-            root = self._parent._h5group
-        root.delete_all([item.id])
+        self._file._h5group.delete_all([item.id])
 
     def __iter__(self):
         for group in self._backend:
@@ -122,8 +119,7 @@ def __delitem__(self, item):
         # the root block
         secids = [s.id for s in item.find_sections()]
 
-        root = self._backend.file
-        root.delete_all(secids)
+        self._file._h5group.delete_all(secids)
 
 
 class SourceContainer(Container):
@@ -146,9 +142,7 @@ def __delitem__(self, item):
         # the root block
         srcids = [s.id for s in item.find_sources()]
         srcids.append(item.id)
-
-        root = self._backend.h5root
-        root.delete_all(srcids)
+        self._file._h5group.delete_all(srcids)
 
 
 class LinkContainer(Container):

nixio/hdf5/h5group.py

@@ -12,11 +12,8 @@
 
 from .h5dataset import H5DataSet
 from ..datatype import DataType
-from ..block import Block
-from ..section import Section
 
 from .. import util
-from ..exceptions import InvalidEntity
 
 
 class H5Group(object):
@@ -297,56 +294,6 @@ def change_id(_, igrp):
             g.visititems(change_id)
         return g
 
-    @property
-    def file(self):
-        """
-        An H5Group object which represents the file root.
-
-        :return: H5Group at '/'
-        """
-        return H5Group(self.group.file, "/", create=False)
-
-    @property
-    def h5root(self):
-        """
-        Returns the H5Group of the Block or top-level Section which contains
-        this object. Returns None if requested on the file root '/' or the
-        /data or /metadata groups.
-
-        :return: Top level object containing this group (H5Group)
-        """
-        pathparts = self.group.name.split("/")
-        if len(pathparts) == 3:
-            return self
-        if self.group.name == "/":
-            return None
-        if len(pathparts) == 2:
-            return None
-
-        return self.parent.h5root
-
-    @property
-    def root(self):
-        """
-        Returns the Block or top-level Section which contains this object.
-        Returns None if requested on the file root '/' or the /data or
-        /metadata groups.
-
-        :return: Top level object containing this group (Block or Section)
-        """
-        h5root = self.h5root
-        if h5root is None:
-            return None
-        topgroup = self.group.name.split("/")[1]
-        if topgroup == "data":
-            cls = Block
-            return cls(h5root.parent, h5root)
-        elif topgroup == "metadata":
-            cls = Section
-            return cls(h5root.parent, h5root)
-        else:
-            raise InvalidEntity
-
     @property
     def parent(self):
         return self.create_from_h5obj(self._parent)

nixio/section.py

@@ -293,9 +293,8 @@ def parent(self):
         """
         if self._sec_parent is not None:
             return self._sec_parent
-        rootmd = self._h5group.file.open_group("metadata")
         # BFS
-        sections = [Section(self.file, None, sg) for sg in rootmd]
+        sections = list(self.file.sections)
         if self in sections:
             # Top-level section
             return None
@@ -309,18 +308,6 @@ def parent(self):
 
         return None
 
-    @property
-    def file(self):
-        """
-        Root file object.
-
-        :type: File
-        """
-        par = self._parent
-        while isinstance(par, Entity):
-            par = par._parent
-        return par
-
     @property
     def referring_objects(self):
         objs = []