########################################################################
#
# License: BSD
# Created: September 4, 2002
# Author: Francesc Alted - faltet@pytables.com
#
# $Id: group.py 4239 2009-09-11 11:28:05Z faltet $
#
########################################################################
"""Here is defined the Group class.
See Group class docstring for more info.
Classes:
Group
RootGroup
TransactionGroupG
TransactionG
MarkG
Functions:
Misc variables:
__version__
"""
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,
HDF5ExtError)
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
from tables.attributeset import AttributeSet
__version__ = "$Revision: 4239 $"
obversion = "1.0"
class _ChildrenDict(tables.misc.proxydict.ProxyDict):
def _getValueFromContainer(self, container, key):
return container._f_getChild(key)
class Group(hdf5Extension.Group, Node):
"""
Basic PyTables grouping structure.
Instances of this class are grouping structures containing *child*
instances of zero or more groups or leaves, together with supporting
metadata. Each group has exactly one *parent* group.
Working with groups and leaves is similar in many ways to working
with directories and files, respectively, in a Unix filesystem. As
with Unix directories and files, objects in the object tree are
often described by giving their full (or absolute) path names. This
full path can be specified either as a string (like in
'/group1/group2') or as a complete object path written in *natural
naming* schema (like in ``file.root.group1.group2``).
A collateral effect of the *natural naming* schema is that the names
of members in the ``Group`` class and its instances must be
carefully chosen to avoid colliding with existing children node
names. For this reason and to avoid polluting the children
namespace all members in a ``Group`` start with some reserved
prefix, like ``_f_`` (for public methods), ``_g_`` (for private
ones), ``_v_`` (for instance variables) or ``_c_`` (for class
variables). Any attempt to create a new child node whose name starts
with one of these prefixes will raise a ``ValueError`` exception.
Another effect of natural naming is that children named after Python
keywords or having names not valid as Python identifiers (e.g.
``class``, ``$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).
Public instance variables
-------------------------
The following instance variables are provided in addition to those
in `Node`:
_v_children
Dictionary with all nodes hanging from this group.
_v_filters
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. When the group has no such
attribute, a default `Filters` instance is used.
_v_groups
Dictionary with all groups hanging from this group.
_v_hidden
Dictionary with all hidden nodes hanging from this group.
_v_leaves
Dictionary with all leaves hanging from this group.
_v_nchildren
The number of children hanging from this group.
Public methods
--------------
.. admonition:: Caveat
The following methods are documented for completeness, and they
can be used without any problem. However, you should use the
high-level counterpart methods in the `File` class, because they
are most used in documentation and examples, and are a bit more
powerful than those exposed here.
The following methods are provided in addition to those in `Node`:
* _f_close()
* _f_copy([newparent][, newname][, overwrite][, recursive][, createparents][, **kwargs])
* _f_copyChildren(dstgroup[, overwrite][, recursive][, createparents][, **kwargs])
* _f_getChild(childname)
* _f_iterNodes([classname])
* _f_listNodes([classname])
* _f_walkGroups()
* _f_walkNodes([classname][, recursive])
Special methods
---------------
Following are described the methods that automatically trigger
actions when a ``Group`` instance is accessed in a special way.
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::
nchild = group._v_nchildren # get a Python attribute
# 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
* __contains__(name)
* __delattr__(name)
* __getattr__(name)
* __iter__()
* __repr__()
* __setattr__(name, value)
* __str__()
"""
# 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_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. 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):
"""Create the basic structures to keep group information.
title -- The title for this group
new -- If this group is new or has to be read from disk
filters -- A Filters instance
"""
# 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_hidden.containerRef = selfRef
super(Group, self).__del__()
def _g_getChildGroupClass(self, childName, warn=True):
"""
Get the class of a not-yet-loaded group child.
`childName` must be the name of a *group* child. If the child
belongs to an unknown kind of group, or if it lacks a ``CLASS``
attribute, `Group` will be returned and a warning will be issued
if `warn` is true and the node belongs to a PyTables file.
"""
childCID = self._g_getGChildAttr(childName, 'CLASS')
if childCID in classIdDict:
return classIdDict[childCID] # look up group class
else:
if warn and self._v_file._isPTFile:
# All kinds of groups in a PyTables file should have
# a known ``CLASS`` attribute value.
warnings.warn(
"group ``%s`` has an unknown class ID ``%s``; "
"it will become a standard ``Group`` node"
% (self._g_join(childName), childCID))
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 thisgroup.Dictionarywithallgroupshangingthisgroup.Dictionarywithallleaveshangingthisgroup.Dictionarywithallhiddennodeshangingthisgroup.Checkwhetherachildrenofitstype. import
Iterate over child nodes hanging directly from thegroup. import
This iterator is *not* recursive. Example of use::
# 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 descendent 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
`Group._f_walkGroups()`, yielding only groups. If you don't
want a recursive behavior, use `Group._f_iterNodes()` instead.
Example of use::
# Recursively print all the arrays hanging from '/'
print \"Arrays in the object tree '/':\"
for array in h5file.root._f_walkNodes('Array'):
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 `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).
if 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, 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_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)
# 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 thisoneintothespecified import
`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 the `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 `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 Nodesuppliedthe import
`classname` parameter, only instances of that class (or
subclasses of it) will be returned.
This is an iterator version of `Group._f_listNodes()`.
"""
self._g_checkOpen()
if not classname:
# Returns all the children alphanumerically sorted
names = self._v_children.keys()
names.sort()
for name in names:
yield self._v_children[name]
elif classname == 'Group':
# Returns all the groups alphanumerically sorted
names = self._v_groups.keys()
names.sort()
for name in names:
yield self._v_groups[name]
elif classname == 'Leaf':
# Returns all the leaves alphanumerically sorted
names = self._v_leaves.keys()
names.sort()
for name in names:
yield self._v_leaves[name]
elif classname == 'IndexArray':
raise TypeError(
"listing ``IndexArray`` nodes is not allowed")
else:
class_ = getClassByName(classname)
children = self._v_children
childNames = children.keys()
childNames.sort()
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 = objgroup._v_groups.keys()
# Sort the groups before delivering. This uses the groups names
# for groups in tree (in order to sort() can classify them).
groupnames.sort()
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 import
object. It does *not* remove children nodes from thisgroup import
for that, use `File.removeNode()` or `Node._f_remove()`. It
does *neither* delete a PyTables node attribute; for that, use
`File.delNodeAttr()`, `Node._f_delAttr()` or `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).
It does *neither* store a PyTables node attribute; for that, use
`File.setNodeAttr()`, `Node._f_setAttr()` or `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 `File.getNode()`, `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 `Node._f_close()`. It
should be noted that this operation closes all the nodes
descending from thisgroup. import
You should not need to close nodes manually because they are
automatically opened/closed when they are loaded/evicted from import
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):
"""Remove (recursively if needed) the Group.
This version correctly handles both visible and hidden nodes.
"""
if self._v_nchildren > 0:
if not recursive:
raise NodeError("group ``%s`` has child nodes; "
"please state recursive removal 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)
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 `Node._f_copy()`. In
addition, it recognizes the following keyword arguments:
`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`
Specifying this parameter overrides the original filter
properties in the source node. If specified, it must be an
instance of the `Filters` class. The default is to copy the
filter properties from thesourcenode. import
`copyuserattrs`
You can prevent the user attributes from beingcopiedby import
setting this parameter 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 whith keys
``'groups'``, ``'leaves'`` and ``'bytes'`` having a numeric
value. Their values will be 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 thisgrouparecopiedinto import
`dstgroup`, which can be a `Group` 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 thisoneunlessoverwritetrue import
this case, the former child node is recursively removed before
copying the later.
By default, nodes descending from childrengroupsofthisnode import
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 subsampled, 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.
Example of use::
>>> f=tables.openFile('data/test.h5')
>>> print f.root.group0
/group0 (Group) 'First Group'</screen>
"""
# Get the associated filename
filename = self._v_file.filename
# The pathname
pathname = self._v_pathname
# Get this class name
classname = self.__class__.__name__
# The title
title = self._v_title
return "%s (%s) %r" % (pathname, classname, title)
def __repr__(self):
"""
Return a detailed string representation of the group.
Example of use::
>>> 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.items() ]
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)
# 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, warn=True)
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)
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)
# 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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