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# -*- coding: utf-8 -*-
########################################################################
#
# License: BSD
# Created: September 4, 2002
# Author: Francesc Alted - faltet@pytables.com
#
# $Id$
#
########################################################################
"""Here is defined the Group class."""
import warnings
import weakref
import tables.misc.proxydict
from tables import hdf5Extension
from tables import utilsExtension
from tables.registry import classIdDict
from tables.exceptions import (
NodeError, NoSuchNodeError, NaturalNameWarning, PerformanceWarning)
from tables.filters import Filters
from tables.registry import getClassByName
from tables.path import checkNameValidity, joinPath, isVisibleName
from tables.node import Node, NotLoggedMixin
from tables.leaf import Leaf
from tables.unimplemented import UnImplemented, Unknown
from tables.link import Link, SoftLink, ExternalLink
obversion = "1.0"
class _ChildrenDict(tables.misc.proxydict.ProxyDict):
def _getValueFromContainer(self, container, key):
return container._f_getChild(key)
class Group(hdf5Extension.Group, Node):
"""Basic PyTables grouping structure.
Instances of this class are grouping structures containing *child*
instances of zero or more groups or leaves, together with supporting
metadata. Each group has exactly one *parent* group.
Working with groups and leaves is similar in many ways to working with
directories and files, respectively, in a Unix filesystem. As with Unix
directories and files, objects in the object tree are often described by
giving their full (or absolute) path names. This full path can be specified
either as a string (like in '/group1/group2') or as a complete object path
written in *natural naming* schema (like in file.root.group1.group2).
A collateral effect of the *natural naming* schema is that the names of
members in the Group class and its instances must be carefully chosen to
avoid colliding with existing children node names. For this reason and to
avoid polluting the children namespace all members in a Group start with
some reserved prefix, like _f_ (for public methods), _g_ (for private
ones), _v_ (for instance variables) or _c_ (for class variables). Any
attempt to create a new child node whose name starts with one of these
prefixes will raise a ValueError exception.
Another effect of natural naming is that children named after Python
keywords or having names not valid as Python identifiers (e.g. class, $a
or 44) can not be accessed using the node.child syntax. You will be forced
to use node._f_getChild(child) to access them (which is recommended for
programmatic accesses).
You will also need to use _f_getChild() to access an existing child node if
you set a Python attribute in the Group with the same name as that node
(you will get a NaturalNameWarning when doing this).
Parameters
----------
title
The title for this group
new
If this group is new or has to be read from disk
filters : Filters
A Filters instance
Notes
-----
The following documentation includes methods that are automatically called
when a Group instance is accessed in a special way.
For instance, this class defines the __setattr__, __getattr__, and
__delattr__ methods, and they set, get and delete *ordinary Python
attributes* as normally intended. In addition to that, __getattr__ allows
getting *child nodes* by their name for the sake of easy interaction on the
command line, as long as there is no Python attribute with the same
name. Groups also allow the interactive completion (when using readline) of
the names of child nodes. For instance::
# get a Python attribute
nchild = group._v_nchildren
# Add a Table child called 'table' under 'group'.
h5file.createTable(group, 'table', myDescription)
table = group.table # get the table child instance
group.table = 'foo' # set a Python attribute
# (PyTables warns you here about using the name of a child node.)
foo = group.table # get a Python attribute
del group.table # delete a Python attribute
table = group.table # get the table child instance again
.. rubric:: Group attributes
The following instance variables are provided in addition to those
in Node (see :ref:`NodeClassDescr`):
.. attribute:: _v_children
Dictionary with all nodes hanging from this group.
.. attribute:: _v_groups
Dictionary with all groups hanging from this group.
.. attribute:: _v_hidden
Dictionary with all hidden nodes hanging from this group.
.. attribute:: _v_leaves
Dictionary with all leaves hanging from this group.
.. attribute:: _v_links
Dictionary with all links hanging from this group.
.. attribute:: _v_unknown
Dictionary with all unknown nodes hanging from this group.
"""
# Class identifier.
_c_classId = 'GROUP'
# Children containers that should be loaded only in a lazy way.
# These are documented in the ``Group._g_addChildrenNames`` method.
_c_lazy_children_attrs = (
'__members__', '_v_children', '_v_groups', '_v_leaves',
'_v_links', '_v_unknown', '_v_hidden')
# <properties>
# `_v_nchildren` is a direct read-only shorthand
# for the number of *visible* children in a group.
def _g_getnchildren(self):
return len(self._v_children)
_v_nchildren = property(_g_getnchildren, None, None,
"The number of children hanging from this group.")
# `_v_filters` is a direct read-write shorthand for the ``FILTERS``
# attribute with the default `Filters` instance as a default value.
def _g_getfilters(self):
filters = getattr(self._v_attrs, 'FILTERS', None)
if filters is None:
filters = Filters()
return filters
def _g_setfilters(self, value):
if not isinstance(value, Filters):
raise TypeError(
"value is not an instance of `Filters`: %r" % (value,))
self._v_attrs.FILTERS = value
def _g_delfilters(self):
del self._v_attrs.FILTERS
_v_filters = property(
_g_getfilters, _g_setfilters, _g_delfilters,
"""Default filter properties for child nodes.
You can (and are encouraged to) use this property to get, set and
delete the FILTERS HDF5 attribute of the group, which stores a Filters
instance (see :ref:`FiltersClassDescr`). When the group has no such
attribute, a default Filters instance is used.
""" )
# </properties>
def __init__(self, parentNode, name,
title="", new=False, filters=None,
_log=True):
# Remember to assign these values in the root group constructor
# if it does not use this one!
# First, set attributes belonging to group objects.
self._v_version = obversion
"""The object version of this group."""
self._v_new = new
"""Is this the first time the node has been created?"""
self._v_new_title = title
"""New title for this node."""
self._v_new_filters = filters
"""New default filter properties for child nodes."""
self._v_maxGroupWidth = parentNode._v_file.params['MAX_GROUP_WIDTH']
"""Maximum number of children on each group before warning the user."""
# Finally, set up this object as a node.
super(Group, self).__init__(parentNode, name, _log)
def _g_postInitHook(self):
if self._v_new:
if self._v_file.params['PYTABLES_SYS_ATTRS']:
# Save some attributes for the new group on disk.
setAttr = self._v_attrs._g__setattr
# Set the title, class and version attributes.
setAttr('TITLE', self._v_new_title)
setAttr('CLASS', self._c_classId)
setAttr('VERSION', self._v_version)
# Set the default filter properties.
newFilters = self._v_new_filters
if newFilters is None:
# If no filters have been passed in the constructor,
# inherit them from the parent group, but only if they
# have been inherited or explicitly set.
newFilters = getattr(
self._v_parent._v_attrs, 'FILTERS', None)
if newFilters is not None:
setAttr('FILTERS', newFilters)
else:
# If the file has PyTables format, get the VERSION attr
if 'VERSION' in self._v_attrs._v_attrnamessys:
self._v_version = self._v_attrs.VERSION
else:
self._v_version = "0.0 (unknown)"
# We don't need to get more attributes from disk,
# since the most important ones are defined as properties.
def __del__(self):
if (self._v_isopen and
self._v_pathname in self._v_file._aliveNodes and
'_v_children' in self.__dict__):
# The group is going to be killed. Rebuild weak references
# (that Python cancelled just before calling this method) so
# that they are still usable if the object is revived later.
selfRef = weakref.ref(self)
self._v_children.containerRef = selfRef
self._v_groups.containerRef = selfRef
self._v_leaves.containerRef = selfRef
self._v_links.containerRef = selfRef
self._v_unknown.containerRef = selfRef
self._v_hidden.containerRef = selfRef
super(Group, self).__del__()
def _g_getChildGroupClass(self, childName):
"""Get the class of a not-yet-loaded group child.
`childName` must be the name of a *group* child.
"""
childCID = self._g_getGChildAttr(childName, 'CLASS')
if childCID in classIdDict:
return classIdDict[childCID] # look up group class
else:
return Group # default group class
def _g_getChildLeafClass(self, childName, warn=True):
"""Get the class of a not-yet-loaded leaf child.
`childName` must be the name of a *leaf* child. If the child
belongs to an unknown kind of leaf, or if its kind can not be
guessed, `UnImplemented` will be returned and a warning will be
issued if `warn` is true.
"""
if self._v_file.params['PYTABLES_SYS_ATTRS']:
childCID = self._g_getLChildAttr(childName, 'CLASS')
else:
childCID = None
if childCID in classIdDict:
return classIdDict[childCID] # look up leaf class
else:
# Unknown or no ``CLASS`` attribute, try a guess.
childCID2 = utilsExtension.whichClass(
self._v_objectID, childName)
if childCID2 == 'UNSUPPORTED':
if warn:
if childCID is None:
warnings.warn(
"leaf ``%s`` is of an unsupported type; "
"it will become an ``UnImplemented`` node"
% self._g_join(childName))
else:
warnings.warn(
("leaf ``%s`` has an unknown class ID ``%s``; "
"it will become an ``UnImplemented`` node")
% (self._g_join(childName), childCID))
return UnImplemented
assert childCID2 in classIdDict
return classIdDict[childCID2] # look up leaf class
def _g_addChildrenNames(self):
"""Add children names to this group taking into account their
visibility and kind.
"""
myDict = self.__dict__
# The names of the lazy attributes
myDict['__members__'] = members = []
"""The names of visible children nodes for readline-style completion."""
myDict['_v_children'] = children = _ChildrenDict(self)
"""The number of children hanging from this group."""
myDict['_v_groups'] = groups = _ChildrenDict(self)
"""Dictionary with all groups hanging from this group."""
myDict['_v_leaves'] = leaves = _ChildrenDict(self)
"""Dictionary with all leaves hanging from this group."""
myDict['_v_links'] = links = _ChildrenDict(self)
"""Dictionary with all links hanging from this group."""
myDict['_v_unknown'] = unknown = _ChildrenDict(self)
"""Dictionary with all unknown nodes hanging from this group."""
myDict['_v_hidden'] = hidden = _ChildrenDict(self)
"""Dictionary with all hidden nodes hanging from this group."""
# Get the names of *all* child groups and leaves.
(groupNames, leafNames, linkNames, unknownNames) = \
self._g_listGroup(self._v_parent)
# Separate groups into visible groups and hidden nodes,
# and leaves into visible leaves and hidden nodes.
for (childNames, childDict) in (
(groupNames, groups),
(leafNames, leaves),
(linkNames, links),
(unknownNames, unknown)):
for childName in childNames:
# See whether the name implies that the node is hidden.
# (Assigned values are entirely irrelevant.)
if isVisibleName(childName):
# Visible node.
members.insert(0, childName)
children[childName] = None
childDict[childName] = None
else:
# Hidden node.
hidden[childName] = None
def _g_checkHasChild(self, name):
"""Check whether 'name' is a children of 'self' and return its type."""
# Get the HDF5 name matching the PyTables name.
node_type = self._g_get_objinfo(name)
if node_type == "NoSuchNode":
raise NoSuchNodeError(
"group ``%s`` does not have a child named ``%s``"
% (self._v_pathname, name))
return node_type
def __iter__(self):
"""Iterate over the child nodes hanging directly from the group.
This iterator is *not* recursive.
Examples
--------
::
# Non-recursively list all the nodes hanging from '/detector'
print "Nodes in '/detector' group:"
for node in h5file.root.detector:
print node
"""
return self._f_iterNodes()
def __contains__(self, name):
"""Is there a child with that `name`?
Returns a true value if the group has a child node (visible or
hidden) with the given `name` (a string), false otherwise.
"""
self._g_checkOpen()
try:
self._g_checkHasChild(name)
except NoSuchNodeError:
return False
return True
def _f_walkNodes(self, classname=None):
"""Iterate over descendant nodes.
This method recursively walks *self* top to bottom (preorder),
iterating over child groups in alphanumerical order, and yielding
nodes. If classname is supplied, only instances of the named class are
yielded.
If *classname* is Group, it behaves like :meth:`Group._f_walkGroups`,
yielding only groups. If you don't want a recursive behavior,
use :meth:`Group._f_iterNodes` instead.
Examples
--------
::
# Recursively print all the arrays hanging from '/'
print "Arrays in the object tree '/':"
for array in h5file.root._f_walkNodes('Array', recursive=True):
print array
"""
self._g_checkOpen()
# For compatibility with old default arguments.
if classname == '':
classname = None
if classname == "Group":
# Recursive algorithm
for group in self._f_walkGroups():
yield group
else:
for group in self._f_walkGroups():
for leaf in group._f_iterNodes(classname):
yield leaf
def _g_join(self, name):
"""Helper method to correctly concatenate a name child object
with the pathname of this group."""
if name == "/":
# This case can happen when doing copies
return self._v_pathname
return joinPath(self._v_pathname, name)
def _g_widthWarning(self):
"""Issue a :exc:`PerformanceWarning` on too many children."""
warnings.warn("""\
group ``%s`` is exceeding the recommended maximum number of children (%d); \
be ready to see PyTables asking for *lots* of memory and possibly slow I/O."""
% (self._v_pathname, self._v_maxGroupWidth),
PerformanceWarning)
def _g_refNode(self, childNode, childName, validate=True):
"""Insert references to a `childNode` via a `childName`.
Checks that the `childName` is valid and does not exist, then
creates references to the given `childNode` by that `childName`.
The validation of the name can be omitted by setting `validate`
to a false value (this may be useful for adding already existing
nodes to the tree).
"""
# Check for name validity.
if validate:
checkNameValidity(childName)
childNode._g_checkName(childName)
# Check if there is already a child with the same name.
# This can be triggered because of the user
# (via node construction or renaming/movement).
# Links are not checked here because they are copied and referenced
# using ``File.getNode`` so they already exist in `self`.
if (not isinstance(childNode, Link)) and childName in self:
raise NodeError(
"group ``%s`` already has a child node named ``%s``"
% (self._v_pathname, childName))
# Show a warning if there is an object attribute with that name.
if childName in self.__dict__:
warnings.warn(
"group ``%s`` already has an attribute named ``%s``; "
"you will not be able to use natural naming "
"to access the child node"
% (self._v_pathname, childName), NaturalNameWarning)
# Check group width limits.
if len(self._v_children) + len(self._v_hidden) >= self._v_maxGroupWidth:
self._g_widthWarning()
# Update members information.
# Insert references to the new child.
# (Assigned values are entirely irrelevant.)
if isVisibleName(childName):
# Visible node.
self.__members__.insert(0, childName) # enable completion
self._v_children[childName] = None # insert node
if isinstance(childNode, Unknown):
self._v_unknown[childName] = None
elif isinstance(childNode, Link):
self._v_links[childName] = None
elif isinstance(childNode, Leaf):
self._v_leaves[childName] = None
elif isinstance(childNode, Group):
self._v_groups[childName] = None
else:
# Hidden node.
self._v_hidden[childName] = None # insert node
def _g_unrefNode(self, childName):
"""Remove references to a node.
Removes all references to the named node.
"""
# This can *not* be triggered because of the user.
assert childName in self, \
("group ``%s`` does not have a child node named ``%s``"
% (self._v_pathname, childName))
# Update members information, if needed
if '_v_children' in self.__dict__:
if childName in self._v_children:
# Visible node.
members = self.__members__
memberIndex = members.index(childName)
del members[memberIndex] # disables completion
del self._v_children[childName] # remove node
self._v_unknown.pop(childName, None)
self._v_links.pop(childName, None)
self._v_leaves.pop(childName, None)
self._v_groups.pop(childName, None)
else:
# Hidden node.
del self._v_hidden[childName] # remove node
def _g_move(self, newParent, newName):
# Move the node to the new location.
oldPath = self._v_pathname
super(Group, self)._g_move(newParent, newName)
newPath = self._v_pathname
# Update location information in children. This node shouldn't
# be affected since it has already been relocated.
self._v_file._updateNodeLocations(oldPath, newPath)
def _g_copy(self, newParent, newName, recursive, _log=True, **kwargs):
# Compute default arguments.
title = kwargs.get('title', self._v_title)
filters = kwargs.get('filters', None)
stats = kwargs.get('stats', None)
# Fix arguments with explicit None values for backwards compatibility.
if title is None: title = self._v_title
# If no filters have been passed to the call, copy them from the
# source group, but only if inherited or explicitly set.
if filters is None:
filters = getattr(self._v_attrs, 'FILTERS', None)
# Create a copy of the object.
newNode = Group(newParent, newName,
title, new=True, filters=filters, _log=_log)
# Copy user attributes if needed.
if kwargs.get('copyuserattrs', True):
self._v_attrs._g_copy(newNode._v_attrs, copyClass=True)
# Update statistics if needed.
if stats is not None:
stats['groups'] += 1
if recursive:
# Copy child nodes if a recursive copy was requested.
# Some arguments should *not* be passed to children copy ops.
kwargs = kwargs.copy()
kwargs.pop('title', None)
self._g_copyChildren(newNode, **kwargs)
return newNode
def _g_copyChildren(self, newParent, **kwargs):
"""Copy child nodes.
Copies all nodes descending from this one into the specified
`newParent`. If the new parent has a child node with the same
name as one of the nodes in this group, the copy fails with a
`NodeError`, maybe resulting in a partial copy. Nothing is
logged.
"""
# Recursive version of children copy.
##for srcChild in self._v_children.itervalues():
## srcChild._g_copyAsChild(newParent, **kwargs)
# Non-recursive version of children copy.
parentStack = [(self, newParent)] # [(source, destination), ...]
while parentStack:
(srcParent, dstParent) = parentStack.pop()
for srcChild in srcParent._v_children.itervalues():
dstChild = srcChild._g_copyAsChild(dstParent, **kwargs)
if isinstance(srcChild, Group):
parentStack.append((srcChild, dstChild))
def _f_getChild(self, childname):
"""Get the child called childname of this group.
If the child exists (be it visible or not), it is returned. Else, a
NoSuchNodeError is raised.
Using this method is recommended over getattr() when doing programmatic
accesses to children if childname is unknown beforehand or when its
name is not a valid Python identifier.
"""
self._g_checkOpen()
self._g_checkHasChild(childname)
childPath = joinPath(self._v_pathname, childname)
return self._v_file._getNode(childPath)
def _f_listNodes(self, classname=None):
"""Return a *list* with children nodes.
This is a list-returning version of :meth:`Group._f_iterNodes()`.
"""
return list(self._f_iterNodes(classname))
def _f_iterNodes(self, classname=None):
"""Iterate over children nodes.
Child nodes are yielded alphanumerically sorted by node name. If the
name of a class derived from Node (see :ref:`NodeClassDescr`) is
supplied in the classname parameter, only instances of that class (or
subclasses of it) will be returned.
This is an iterator version of :meth:`Group._f_listNodes`.
"""
self._g_checkOpen()
if not classname:
# Returns all the children alphanumerically sorted
names = sorted(self._v_children.iterkeys())
for name in names:
yield self._v_children[name]
elif classname == 'Group':
# Returns all the groups alphanumerically sorted
names = sorted(self._v_groups.iterkeys())
for name in names:
yield self._v_groups[name]
elif classname == 'Leaf':
# Returns all the leaves alphanumerically sorted
names = sorted(self._v_leaves.iterkeys())
for name in names:
yield self._v_leaves[name]
elif classname == 'Link':
# Returns all the links alphanumerically sorted
names = sorted(self._v_links.iterkeys())
for name in names:
yield self._v_links[name]
elif classname == 'IndexArray':
raise TypeError(
"listing ``IndexArray`` nodes is not allowed")
else:
class_ = getClassByName(classname)
children = self._v_children
childNames = sorted(children.iterkeys())
for childName in childNames:
childNode = children[childName]
if isinstance(childNode, class_):
yield childNode
def _f_walkGroups(self):
"""Recursively iterate over descendent groups (not leaves).
This method starts by yielding *self*, and then it goes on to
recursively iterate over all child groups in alphanumerical order, top
to bottom (preorder), following the same procedure.
"""
self._g_checkOpen()
stack = [self]
yield self
# Iterate over the descendants
while stack:
objgroup=stack.pop()
groupnames = sorted(objgroup._v_groups.iterkeys())
# Sort the groups before delivering. This uses the groups names
# for groups in tree (in order to sort() can classify them).
for groupname in groupnames:
stack.append(objgroup._v_groups[groupname])
yield objgroup._v_groups[groupname]
def __delattr__(self, name):
"""Delete a Python attribute called name.
This method deletes an *ordinary Python attribute* from the object. It
does *not* remove children nodes from this group; for that,
use :meth:`File.removeNode` or :meth:`Node._f_remove`. It does *neither*
delete a PyTables node attribute; for that,
use :meth:`File.delNodeAttr`, :meth:`Node._f_delAttr`
or :attr:`Node._v_attrs``.
If there is an attribute and a child node with the same name, the child
node will be made accessible again via natural naming.
"""
try:
super(Group, self).__delattr__(name) # nothing particular
except AttributeError, ae:
hint = " (use ``node._f_remove()`` if you want to remove a node)"
raise ae.__class__(str(ae) + hint)
def __getattr__(self, name):
"""Get a Python attribute or child node called name.
If the object has a Python attribute called name, its value is
returned. Else, if the node has a child node called name, it is
returned. Else, an AttributeError is raised.
"""
# That is true since a `NoSuchNodeError` is an `AttributeError`.
myDict = self.__dict__
if name in myDict:
return myDict[name]
elif name in self._c_lazy_children_attrs:
self._g_addChildrenNames()
return myDict[name]
return self._f_getChild(name)
def __setattr__(self, name, value):
"""Set a Python attribute called name with the given value.
This method stores an *ordinary Python attribute* in the object. It
does *not* store new children nodes under this group; for that, use the
File.create*() methods (see the File class
in :ref:`FileClassDescr`). It does *neither* store a PyTables node
attribute; for that,
use :meth:`File.setNodeAttr`, :meth`:Node._f_setAttr`
or :attr:`Node._v_attrs`.
If there is already a child node with the same name, a
NaturalNameWarning will be issued and the child node will not be
accessible via natural naming nor getattr(). It will still be available
via :meth:`File.getNode`, :meth:`Group._f_getChild` and children
dictionaries in the group (if visible).
"""
# Show a warning if there is an child node with that name.
#
# ..note::
#
# Using ``if name in self:`` is not right since that would
# require ``_v_children`` and ``_v_hidden`` to be already set
# when the very first attribute assignments are made.
# Moreover, this warning is only concerned about clashes with
# names used in natural naming, i.e. those in ``__members__``.
#
# ..note::
#
# The check ``'__members__' in myDict`` allows attribute
# assignment to happen before calling `Group.__init__()`, by
# avoiding to look into the still not assigned ``__members__``
# attribute. This allows subclasses to set up some attributes
# and then call the constructor of the superclass. If the
# check above is disabled, that results in Python entering an
# endless loop on exit!
myDict = self.__dict__
if '__members__' in myDict and name in self.__members__:
warnings.warn(
"group ``%s`` already has a child node named ``%s``; "
"you will not be able to use natural naming "
"to access the child node"
% (self._v_pathname, name), NaturalNameWarning)
super(Group, self).__setattr__(name, value)
def _f_flush(self):
"""Flush this Group"""
self._g_checkOpen()
self._g_flushGroup()
def _g_closeDescendents(self):
"""Close all the *loaded* descendent nodes of this group."""
def closeNodes(prefix, nodePaths, getNode):
for nodePath in nodePaths:
if nodePath.startswith(prefix):
try:
node = getNode(nodePath)
# Avoid descendent nodes to also iterate over
# their descendents, which are already to be
# closed by this loop.
if hasattr(node, '_f_getChild'):
node._g_close()
else:
node._f_close()
del node
except KeyError:
pass
prefix = self._v_pathname + '/'
if prefix == '//':
prefix = '/'
# Close all loaded nodes.
aliveNodes = self._v_file._aliveNodes
deadNodes = self._v_file._deadNodes
reviveNode = self._v_file._reviveNode
# First, close the alive nodes and delete them
# so they are not placed in the limbo again.
# These two steps ensure tables are closed *before* their indices.
closeNodes(prefix,
[path for path in aliveNodes
if '/_i_' not in path], # not indices
lambda path: aliveNodes[path])
# Close everything else (i.e. indices)
closeNodes(prefix,
[path for path in aliveNodes],
lambda path: aliveNodes[path])
# Next, revive the dead nodes, close and delete them
# so they are not placed in the limbo again.
# These two steps ensure tables are closed *before* their indices.
closeNodes(prefix,
[path for path in deadNodes
if '/_i_' not in path], # not indices
lambda path: reviveNode(path))
# Close everything else (i.e. indices)
closeNodes(prefix,
[path for path in deadNodes],
lambda path: reviveNode(path))
def _g_close(self):
"""Close this (open) group."""
# hdf5Extension operations:
# Close HDF5 group.
self._g_closeGroup()
# Close myself as a node.
super(Group, self)._f_close()
def _f_close(self):
"""Close this group and all its descendents.
This method has the behavior described in :meth:`Node._f_close`. It
should be noted that this operation closes all the nodes descending
from this group.
You should not need to close nodes manually because they are
automatically opened/closed when they are loaded/evicted from the
integrated LRU cache.
"""
# If the group is already closed, return immediately
if not self._v_isopen:
return
# First, close all the descendents of this group, unless a) the
# group is being deleted (evicted from LRU cache) or b) the node
# is being closed during an aborted creation, in which cases
# this is not an explicit close issued by the user.
if not (self._v__deleting or self._v_objectID is None):
self._g_closeDescendents()
# When all the descendents have been closed, close this group.
# This is done at the end because some nodes may still need to
# be loaded during the closing process; thus this node must be
# open until the very end.
self._g_close()
def _g_remove(self, recursive=False, force=False):
"""Remove (recursively if needed) the Group.
This version correctly handles both visible and hidden nodes.
"""
if self._v_nchildren > 0:
if not (recursive or force):
raise NodeError("group ``%s`` has child nodes; "
"please set `recursive` or `force` to true "
"to remove it"
% (self._v_pathname,))
# First close all the descendents hanging from this group,
# so that it is not possible to use a node that no longer exists.
self._g_closeDescendents()
# Remove the node itself from the hierarchy.
super(Group, self)._g_remove(recursive, force)
def _f_copy(self, newparent=None, newname=None,
overwrite=False, recursive=False, createparents=False,
**kwargs):
"""Copy this node and return the new one.
This method has the behavior described in :meth:`Node._f_copy`.
In addition, it recognizes the following keyword arguments:
Parameters
----------
title
The new title for the destination. If omitted or None, the original
title is used. This only applies to the topmost node in recursive
copies.
filters : Filters
Specifying this parameter overrides the original filter properties
in the source node. If specified, it must be an instance of the
Filters class (see :ref:`FiltersClassDescr`).
The default is to copy the filter properties from the source node.
copyuserattrs
You can prevent the user attributes from being copied by setting
thisparameter to False. The default is to copy them.
stats
This argument may be used to collect statistics on the copy
process. When used, it should be a dictionary with keys 'groups',
'leaves', 'links' and 'bytes' having a numeric value. Their values
willbe incremented to reflect the number of groups, leaves and
bytes, respectively, that have been copied during the operation.
"""
return super(Group, self)._f_copy(
newparent, newname,
overwrite, recursive, createparents, **kwargs)
def _f_copyChildren(self, dstgroup, overwrite=False, recursive=False,
createparents=False, **kwargs):
"""Copy the children of this group into another group.
Children hanging directly from this group are copied into dstgroup,
which can be a Group (see :ref:`GroupClassDescr`) object or its
pathname in string form. If createparents is true, the needed groups
for the given destination group path to exist will be created.
The operation will fail with a NodeError if there is a child node in
the destination group with the same name as one of the copied children
from this one, unless overwrite is true; in this case, the former child
node is recursively removed before copying the later.
By default, nodes descending from children groups of this node are not
copied. If the recursive argument is true, all descendant nodes of this
node are recursively copied.
Additional keyword arguments may be passed to customize the copying
process. For instance, title and filters may be changed, user
attributes may be or may not be copied, data may be sub-sampled, stats
may be collected, etc. Arguments unknown to nodes are simply
ignored. Check the documentation for copying operations of nodes to see
which options they support.
"""
self._g_checkOpen()
# `dstgroup` is used instead of its path to avoid accepting
# `Node` objects when `createparents` is true. Also, note that
# there is no risk of creating parent nodes and failing later
# because of destination nodes already existing.
dstParent = self._v_file._getOrCreatePath(dstgroup, createparents)
self._g_checkGroup(dstParent) # Is it a group?
if not overwrite:
# Abort as early as possible when destination nodes exist
# and overwriting is not enabled.
for childName in self._v_children:
if childName in dstParent:
raise NodeError(
"destination group ``%s`` already has "
"a node named ``%s``; "
"you may want to use the ``overwrite`` argument"
% (dstParent._v_pathname, childName) )
for child in self._v_children.itervalues():
child._f_copy(dstParent, None, overwrite, recursive, **kwargs)
def __str__(self):
"""Return a short string representation of the group.
Examples
--------
::
>>> f=tables.openFile('data/test.h5')
>>> print f.root.group0
/group0 (Group) 'First Group'
"""
pathname = self._v_pathname
classname = self.__class__.__name__
title = self._v_title
return "%s (%s) %r" % (pathname, classname, title)
def __repr__(self):
"""Return a detailed string representation of the group.
Examples
--------
::
>>> f = tables.openFile('data/test.h5')
>>> f.root.group0
/group0 (Group) 'First Group'
children := ['tuple1' (Table), 'group1' (Group)]
"""
rep = [ '%r (%s)' % \
(childname, child.__class__.__name__)
for (childname, child) in self._v_children.iteritems() ]
childlist = '[%s]' % (', '.join(rep))
return "%s\n children := %s" % \
(str(self), childlist)
# Special definition for group root
class RootGroup(Group):
def __init__(self, ptFile, name, title, new, filters):
myDict = self.__dict__
# Set group attributes.
self._v_version = obversion
self._v_new = new
if new:
self._v_new_title = title
self._v_new_filters = filters
else:
self._v_new_title = None
self._v_new_filters = None
# Set node attributes.
self._v_file = ptFile
self._v_isopen = True # root is always open
self._v_pathname = '/'
self._v_name = '/'
self._v_depth = 0
self._v_maxGroupWidth = ptFile.params['MAX_GROUP_WIDTH']
self._v__deleting = False
self._v_objectID = None # later
# Only the root node has the file as a parent.
# Bypass __setattr__ to avoid the ``Node._v_parent`` property.
myDict['_v_parent'] = ptFile
ptFile._refNode(self, '/')
# hdf5Extension operations (do before setting an AttributeSet):
# Update node attributes.
self._g_new(ptFile, name, init=True)
# Open the node and get its object ID.
self._v_objectID = self._g_open()
# Set disk attributes and read children names.
#
# This *must* be postponed because this method needs the root node
# to be created and bound to ``File.root``.
# This is an exception to the rule, handled by ``File.__init()__``.
#
##self._g_postInitHook()
def _g_loadChild(self, childName):
"""Load a child node from disk.
The child node `childName` is loaded from disk and an adequate
`Node` object is created and returned. If there is no such
child, a `NoSuchNodeError` is raised.
"""
if self._v_file.rootUEP != "/":
childName = joinPath(self._v_file.rootUEP, childName)
# Is the node a group or a leaf?
node_type = self._g_checkHasChild(childName)
# Nodes that HDF5 report as H5G_UNKNOWN
if node_type == 'Unknown':
return Unknown(self, childName)
# Guess the PyTables class suited to the node,
# build a PyTables node and return it.
if node_type == "Group":
if self._v_file.params['PYTABLES_SYS_ATTRS']:
childClass = self._g_getChildGroupClass(childName)
else:
# Default is a Group class
childClass = Group
return childClass(self, childName, new=False)
elif node_type == "Leaf":
childClass = self._g_getChildLeafClass(childName, warn=True)
# Building a leaf may still fail because of unsupported types
# and other causes.
###return childClass(self, childName) # uncomment for debugging
try:
return childClass(self, childName)
except Exception, exc: #XXX
warnings.warn(
"problems loading leaf ``%s``::\n\n"
" %s\n\n"
"The leaf will become an ``UnImplemented`` node."
% (self._g_join(childName), exc))
# If not, associate an UnImplemented object to it
return UnImplemented(self, childName)
elif node_type == "SoftLink":
return SoftLink(self, childName)
elif node_type == "ExternalLink":
return ExternalLink(self, childName)
else:
return UnImplemented(self, childName)
def _f_rename(self, newname):
raise NodeError("the root node can not be renamed")
def _f_move(self, newparent=None, newname=None, createparents=False):
raise NodeError("the root node can not be moved")
def _f_remove(self, recursive = False):
raise NodeError("the root node can not be removed")
class TransactionGroupG(NotLoggedMixin, Group):
_c_classId = 'TRANSGROUP'
def _g_widthWarning(self):
warnings.warn("""\
the number of transactions is exceeding the recommended maximum (%d);\
be ready to see PyTables asking for *lots* of memory and possibly slow I/O"""
% (self._v_maxGroupWidth,), PerformanceWarning)
class TransactionG(NotLoggedMixin, Group):
_c_classId = 'TRANSG'
def _g_widthWarning(self):
warnings.warn("""\
transaction ``%s`` is exceeding the recommended maximum number of marks (%d);\
be ready to see PyTables asking for *lots* of memory and possibly slow I/O"""
% (self._v_pathname, self._v_maxGroupWidth),
PerformanceWarning)
class MarkG(NotLoggedMixin, Group):
# Class identifier.
_c_classId = 'MARKG'
import re
_c_shadowNameRE = re.compile(r'^a[0-9]+$')
def _g_widthWarning(self):
warnings.warn("""\
mark ``%s`` is exceeding the recommended maximum action storage (%d nodes);\
be ready to see PyTables asking for *lots* of memory and possibly slow I/O"""
% (self._v_pathname, self._v_maxGroupWidth),
PerformanceWarning)
def _g_reset(self):
"""Empty action storage (nodes and attributes).
This method empties all action storage kept in this node: nodes
and attributes.
"""
# Remove action storage nodes.
for child in self._v_children.values():
child._g_remove(True, True)
# Remove action storage attributes.
attrs = self._v_attrs
shname = self._c_shadowNameRE
for attrname in attrs._v_attrnamesuser[:]:
if shname.match(attrname):
attrs._g__delattr(attrname)
## Local Variables:
## mode: python
## py-indent-offset: 4
## tab-width: 4
## fill-column: 72
## End:
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