"""Create links in the HDF5 file.
This module implements containers for soft and external links. Hard
links doesn't need a container as such as they are the same as regular
nodes (groups or leaves).
Classes:
SoftLink
ExternalLink
Functions:
Misc variables:
"""
from pathlib import Path
import tables as tb
from . import linkextension
from .node import Node
from .utils import lazyattr
from .attributeset import AttributeSet
def _g_get_link_class(parent_id, name):
"""Guess the link class."""
return linkextension._get_link_class(parent_id, name)
[docs]class Link(Node):
"""Abstract base class for all PyTables links.
A link is a node that refers to another node. The Link class inherits from
Node class and the links that inherits from Link are SoftLink and
ExternalLink. There is not a HardLink subclass because hard links behave
like a regular Group or Leaf. Contrarily to other nodes, links cannot have
HDF5 attributes. This is an HDF5 library limitation that might be solved
in future releases.
See :ref:`LinksTutorial` for a small tutorial on how to work with links.
.. rubric:: Link attributes
.. attribute:: target
The path string to the pointed node.
"""
# Properties
@lazyattr
def _v_attrs(self):
"""
A *NoAttrs* instance replacing the typical *AttributeSet* instance of
other node objects. The purpose of *NoAttrs* is to make clear that
HDF5 attributes are not supported in link nodes.
"""
class NoAttrs(AttributeSet):
def __getattr__(self, name):
raise KeyError("you cannot get attributes from this "
"`%s` instance" % self.__class__.__name__)
def __setattr__(self, name, value):
raise KeyError("you cannot set attributes to this "
"`%s` instance" % self.__class__.__name__)
def _g_close(self):
pass
return NoAttrs(self)
def __init__(self, parentnode, name, target=None, _log=False):
self._v_new = target is not None
self.target = target
"""The path string to the pointed node."""
super().__init__(parentnode, name, _log)
# Public and tailored versions for copy, move, rename and remove methods
[docs] def copy(self, newparent=None, newname=None,
overwrite=False, createparents=False):
"""Copy this link and return the new one.
See :meth:`Node._f_copy` for a complete explanation of the arguments.
Please note that there is no recursive flag since links do not have
child nodes.
"""
newnode = self._f_copy(newparent=newparent, newname=newname,
overwrite=overwrite,
createparents=createparents)
# Insert references to a `newnode` via `newname`
newnode._v_parent._g_refnode(newnode, newname, True)
return newnode
[docs] def move(self, newparent=None, newname=None, overwrite=False):
"""Move or rename this link.
See :meth:`Node._f_move` for a complete explanation of the arguments.
"""
return self._f_move(newparent=newparent, newname=newname,
overwrite=overwrite)
[docs] def remove(self):
"""Remove this link from the hierarchy."""
return self._f_remove()
[docs] def rename(self, newname=None, overwrite=False):
"""Rename this link in place.
See :meth:`Node._f_rename` for a complete explanation of the arguments.
"""
return self._f_rename(newname=newname, overwrite=overwrite)
def __repr__(self):
return str(self)
[docs]class SoftLink(linkextension.SoftLink, Link):
"""Represents a soft link (aka symbolic link).
A soft link is a reference to another node in the *same* file hierarchy.
Provided that the target node exists, its attributes and methods can be
accessed directly from the softlink using the normal `.` syntax.
Softlinks also have the following public methods/attributes:
* `target`
* `dereference()`
* `copy()`
* `move()`
* `remove()`
* `rename()`
* `is_dangling()`
Note that these will override any correspondingly named methods/attributes
of the target node.
For backwards compatibility, it is also possible to obtain the target node
via the `__call__()` special method (this action is called *dereferencing*;
see below)
Examples
--------
::
>>> import numpy as np
>>> f = tb.open_file('/tmp/test_softlink.h5', 'w')
>>> a = f.create_array('/', 'A', np.arange(10))
>>> link_a = f.create_soft_link('/', 'link_A', target='/A')
# transparent read/write access to a softlinked node
>>> link_a[0] = -1
>>> link_a[:], link_a.dtype
(array([-1, 1, 2, 3, 4, 5, 6, 7, 8, 9]), dtype('int64'))
# dereferencing a softlink using the __call__() method
>>> link_a() is a
True
# SoftLink.remove() overrides Array.remove()
>>> link_a.remove()
>>> print(link_a)
<closed tables.link.SoftLink at ...>
>>> a[:], a.dtype
(array([-1, 1, 2, 3, 4, 5, 6, 7, 8, 9]), dtype('int64'))
>>> f.close()
"""
# Class identifier.
_c_classid = 'SOFTLINK'
# attributes with these names/prefixes are treated as attributes of the
# SoftLink rather than the target node
_link_attrnames = ('target', 'dereference', 'is_dangling', 'copy', 'move',
'remove', 'rename', '__init__', '__str__', '__repr__',
'__unicode__', '__class__', '__dict__')
_link_attrprefixes = ('_f_', '_c_', '_g_', '_v_')
[docs] def __call__(self):
"""Dereference `self.target` and return the object.
Examples
--------
::
>>> f = tb.open_file('tables/tests/slink.h5')
>>> f.root.arr2
/arr2 (SoftLink) -> /arr
>>> print(f.root.arr2())
/arr (Array(2,)) ''
>>> f.close()
"""
return self.dereference()
def dereference(self):
if self._v_isopen:
target = self.target
# Check for relative pathnames
if not self.target.startswith('/'):
target = self._v_parent._g_join(self.target)
return self._v_file._get_node(target)
else:
return None
def __getattribute__(self, attrname):
# get attribute of the SoftLink itself
if (attrname in SoftLink._link_attrnames or
attrname[:3] in SoftLink._link_attrprefixes):
return object.__getattribute__(self, attrname)
# get attribute of the target node
elif not self._v_isopen:
raise tb.ClosedNodeError('the node object is closed')
elif self.is_dangling():
return None
else:
target_node = self.dereference()
try:
# __getattribute__() fails to get children of Groups
return target_node.__getattribute__(attrname)
except AttributeError:
# some node classes (e.g. Array) don't implement __getattr__()
return target_node.__getattr__(attrname)
def __setattr__(self, attrname, value):
# set attribute of the SoftLink itself
if (attrname in SoftLink._link_attrnames or
attrname[:3] in SoftLink._link_attrprefixes):
object.__setattr__(self, attrname, value)
# set attribute of the target node
elif not self._v_isopen:
raise tb.ClosedNodeError('the node object is closed')
elif self.is_dangling():
raise ValueError("softlink target does not exist")
else:
self.dereference().__setattr__(attrname, value)
def __getitem__(self, key):
"""__getitem__ must be defined in the SoftLink class in order for array
indexing syntax to work"""
if not self._v_isopen:
raise tb.ClosedNodeError('the node object is closed')
elif self.is_dangling():
raise ValueError("softlink target does not exist")
else:
return self.dereference().__getitem__(key)
def __setitem__(self, key, value):
"""__setitem__ must be defined in the SoftLink class in order for array
indexing syntax to work"""
if not self._v_isopen:
raise tb.ClosedNodeError('the node object is closed')
elif self.is_dangling():
raise ValueError("softlink target does not exist")
else:
self.dereference().__setitem__(key, value)
def is_dangling(self):
return not (self.dereference() in self._v_file)
[docs] def __str__(self):
"""Return a short string representation of the link.
Examples
--------
::
>>> f = tb.open_file('tables/tests/slink.h5')
>>> f.root.arr2
/arr2 (SoftLink) -> /arr
>>> f.close()
"""
target = str(self.target)
# Check for relative pathnames
if not self.target.startswith('/'):
target = self._v_parent._g_join(self.target)
closed = "" if self._v_isopen else "closed "
dangling = "" if target in self._v_file else " (dangling)"
return (f"{closed}{self._v_pathname} ({self.__class__.__name__}) -> "
f"{self.target}{dangling}")
[docs]class ExternalLink(linkextension.ExternalLink, Link):
"""Represents an external link.
An external link is a reference to a node in *another* file.
Getting access to the pointed node (this action is called
*dereferencing*) is done via the :meth:`__call__` special method
(see below).
.. rubric:: ExternalLink attributes
.. attribute:: extfile
The external file handler, if the link has been dereferenced.
In case the link has not been dereferenced yet, its value is
None.
"""
# Class identifier.
_c_classid = 'EXTERNALLINK'
def __init__(self, parentnode, name, target=None, _log=False):
self.extfile = None
"""The external file handler, if the link has been dereferenced.
In case the link has not been dereferenced yet, its value is
None."""
super().__init__(parentnode, name, target, _log)
def _get_filename_node(self):
"""Return the external filename and nodepath from `self.target`."""
# This is needed for avoiding the 'C:\\file.h5' filepath notation
filename, target = self.target.split(':/')
return filename, '/' + target
[docs] def __call__(self, **kwargs):
"""Dereference self.target and return the object.
You can pass all the arguments supported by the :func:`open_file`
function (except filename, of course) so as to open the referenced
external file.
Examples
--------
::
>>> f = tb.open_file('tables/tests/elink.h5')
>>> f.root.pep.pep2
/pep/pep2 (ExternalLink) -> elink2.h5:/pep
>>> pep2 = f.root.pep.pep2(mode='r') # open in 'r'ead mode
>>> print(pep2)
/pep (Group) ''
>>> pep2._v_file.filename # belongs to referenced file
'tables/tests/elink2.h5'
>>> f.close()
"""
filename, target = self._get_filename_node()
if not Path(filename).is_absolute():
# Resolve the external link with respect to the this
# file's directory. See #306.
filename = str(Path(self._v_file.filename).with_name(filename))
if self.extfile is None or not self.extfile.isopen:
self.extfile = tb.open_file(filename, **kwargs)
else:
# XXX: implement better consistency checks
assert self.extfile.filename == filename
assert self.extfile.mode == kwargs.get('mode', 'r')
return self.extfile._get_node(target)
[docs] def umount(self):
"""Safely unmount self.extfile, if opened."""
extfile = self.extfile
# Close external file, if open
if extfile is not None and extfile.isopen:
extfile.close()
self.extfile = None
def _f_close(self):
"""Especific close for external links."""
self.umount()
super()._f_close()
[docs] def __str__(self):
"""Return a short string representation of the link.
Examples
--------
::
>>> f = tb.open_file('tables/tests/elink.h5')
>>> f.root.pep.pep2
/pep/pep2 (ExternalLink) -> elink2.h5:/pep
>>> f.close()
"""
return (f"{self._v_pathname} ({self.__class__.__name__}) -> "
f"{self.target}")