python-tables 2.3.1-2ubuntu3 / usr / share / pyshared / tables / nodes / filenode.py

########################################################################
#
#	License: BSD
#	Created: October 2, 2004
#	Author:  Ivan Vilata i Balaguer - reverse:net.selidor@ivan
#
#	$Source: /home/ivan/_/programari/pytables/svn/cvs/pytables/pytables/tables/nodes/FileNode.py,v $
#	$Id$
#
########################################################################

"""A file interface to nodes for PyTables databases.

The FileNode module provides a file interface for using inside of
PyTables database files.  Use the newNode() function to create a brand
new file node which can be read and written as any ordinary Python
file.  Use the openNode() function to open an existing (i.e. created
with newNode()) node for read-only or read-write access.  Read acces
is always available.  Write access (enabled on new files and files
opened with mode 'a+') only allows appending data to a file node.


Constants:
	NodeType         -- Value for 'NODE_TYPE' node system attribute.
	NodeTypeVersions -- Supported values for 'NODE_TYPE_VERSION'
	                    node system attribute.
"""

import os, warnings

import numpy

import tables



__revision__ = '$Id$'

NodeType         = 'file'
NodeTypeVersions = [1, 2]



def newNode(h5file, **kwargs):
	"""newNode(file, ...) -> file node object.  Creates a new file node.

	Creates a new file node object in the specified PyTables file object.
	Additional named arguments 'where' and 'name' must be passed
	to specify where the file node is to be created.
	Other named arguments such as 'title' and 'filters' may also be passed.

	The special named argument 'expectedsize', indicating an estimate
	of the file size in bytes, may also be passed.
	"""

	return RAFileNode(None, h5file, **kwargs)



def openNode(node, mode = 'r'):
	"""openNode(node[, mode]) -> file node object.  Opens an existing file node.

	Returns a file node object from the existing specified PyTables node.
	If mode is not specified or it is 'r', the file can only be read,
	and the pointer is positioned at the beginning of the file.
	If mode is 'a+', the file can be read and appended,
	and the pointer is positioned at the end of the file.
	"""

	if mode == 'r':
		return ROFileNode(node)
	elif mode == 'a+':
		return RAFileNode(node, None)
	else:
		raise IOError("invalid mode: %s" % (mode,))



class ReadableMixin:
	"""Mix-in class which provides reading methods for readable file nodes.

	It also defines the 'lineSeparator' property,
	which contains the string used as a line separator,
	and defaults to os.linesep.
	It can be set to any reasonably-sized string you want.

	This class requires support for:
		* 'offset' and 'node' attributes
		* _checkNotClosed() and seek() methods
	"""

	# The number of bytes readline() reads at a time.
	_lineChunkSize = 128


	# The line separator string.
	_lineSeparator = os.linesep

	# The line separator string property methods.
	def getLineSeparator(self):
		"getLineSeparator() -> string.  Gets the line separator string."

		return self._lineSeparator

	def setLineSeparator(self, value):
		"""setLineSeparator(string) -> None.  Sets the line separator string.

		Raises ValueError if the string is empty or too long.
		"""

		if value == '':
			raise ValueError("line separator string is empty")
		elif len(value) > self._lineChunkSize:
			raise ValueError("sorry, line separator string is too long")
		else:
			self._lineSeparator = value

	def delLineSeparator(self):
		"delLineSeparator() -> None.  Deletes the 'lineSeparator' property."

		del self._lineSeparator

	# The line separator string property.
	lineSeparator = property(
		getLineSeparator, setLineSeparator, delLineSeparator,
		"A property containing the line separator string.")


	def __iter__(self):
		return self


	def next(self):
		"""next() -> string.  Gets the next line of text.

		Raises StopIteration when finished.
		See file.next.__doc__ for more information.
		"""

		# The use of this method is compatible with the use of readline().
		line = self.readline()
		if len(line) == 0:
			raise StopIteration
		return line


	def read(self, size = None):
		"""read([size]) -> string.  Reads at most 'size' bytes.

		See file.read.__doc__ for more information.
		"""

		self._checkNotClosed()

		# 2004-08-03: Reading from beyond the last row raises an IndexError.
		#   Moreover, the pointer should not be incremented.
		if self.offset >= self.node.nrows:
			return ''

		start = self.offset
		if size is None or size < 0:
			# Read the entire file.
			# 2004-08-03: A None value would only read one row.
			stop = self.node.nrows
		else:
			# Read the specified number of rows, if available.
			# 2004-08-04: Reading beyond the last row is allowed.
			stop = self.offset + size

		data = self.node.read(start, stop).tostring()
		self.offset += len(data)
		return data


	def readline(self, size = -1):
		"""readline([size]) -> string.  Reads the next text line.

		See file.readline.__doc__ for more information.
		"""

		self._checkNotClosed()

		# Set the remaining bytes to read to the specified size.
		remsize = size

		lseplen = len(self._lineSeparator)
		partial = []
		finished = False

		while not finished:
			# Read a string limited by the remaining number of bytes.
			if size <= 0:
				ibuff = self.read(self._lineChunkSize)
			else:
				ibuff = self.read(min(remsize, self._lineChunkSize))
			ibufflen = len(ibuff)
			remsize -= ibufflen

			if ibufflen >= lseplen:
				# Separator fits, look for EOL string.
				eolindex = ibuff.find(self._lineSeparator)
			elif ibufflen == 0:
				# EOF was immediately reached.
				finished = True
				continue
			else:  # ibufflen < lseplen
				# EOF was hit and separator does not fit. ;)
				partial.append(ibuff)
				finished = True
				continue

			if eolindex >= 0:
				# Found an EOL. If there are trailing characters,
				# cut the input buffer and seek back;
				# else add the whole input buffer.
				trailing = ibufflen - lseplen - eolindex  # Bytes beyond EOL.
				if trailing > 0:
					obuff = ibuff[:-trailing]
					self.seek(-trailing, 1)
					remsize += trailing
				else:
					obuff = ibuff
				finished = True
			elif lseplen > 1 and (size <= 0 or remsize > 0):
				# Seek back a little since the end of the read string
				# may have fallen in the middle of the line separator.
				obuff = ibuff[:-lseplen + 1]
				self.seek(-lseplen + 1, 1)
				remsize += lseplen - 1
			else:  # eolindex<0 and (lseplen<=1 or (size>0 and remsize<=0))
				# Did not find an EOL, add the whole input buffer.
				obuff = ibuff

			# Append (maybe cut) buffer.
			partial.append(obuff)

			# If a size has been specified and the remaining count
			# reaches zero, the reading is finished.
			if size > 0 and remsize <= 0:
				finished = True

		return ''.join(partial)


	def readlines(self, sizehint = -1):
		"""readlines([sizehint]) -> list of strings.  Reads the text lines.

		See file.readlines.__doc__ for more information.
		"""

		# Set the remaining bytes to read to the size hint.
		remsize = sizehint

		lines = []
		finished = False

		while not finished:
			# Read a line limited by the remaining number of bytes.
			if sizehint <= 0:
				line = self.readline()
			else:
				line = self.readline(remsize)
			remsize -= len(line)

			# An empty line finishes the reading.
			if len(line) > 0:
				lines.append(line)
			else:
				finished = True
				continue

			# If a size hint has been specified and the remaining count
			# reaches zero, the reading is finished.
			if sizehint > 0 and remsize <= 0:
				finished = True

		return lines


	def xreadlines(self):
		"""xreadlines() -> self.  For backward compatibility.

		See file.xreadlines.__doc__ for more information.
		"""

		return self



class NotReadableMixin:
	"""Mix-in class which provides reading methods for non-readable file nodes.

	This class requires support for:
		* _checkNotClosed() method
	"""

	def _notReadableError(self):
		"""_notReadableError() -> None

		Raises a common IOError exception for non-readable file nodes.
		"""
		raise IOError("the file is not readable")


	# The definition of those methods may seem odd
	# but it is the way Python (2.3) files work.

	def __iter__(self):
		return self


	def next(self):
		"""next() -> string.  Gets the next line of text.

		Raises IOError.
		See file.next.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notReadableError()


	def read(self, size = None):
		"""read([size]) -> string.  Reads at most 'size' bytes.

		Raises IOError.
		See file.read.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notReadableError()


	def readline(self, size = -1):
		"""readline([size]) -> string.  Reads the next text line.

		Raises IOError.
		See file.readline.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notReadableError()


	def readlines(self, sizehint = -1):
		"""readlines([sizehint]) -> list of strings.  Reads the text lines.

		Raises IOError.
		See file.readlines.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notReadableError()


	def xreadlines(self):
		"""xreadlines() -> self.  For backward compatibility.

		See file.xreadlines.__doc__ for more information.
		"""

		return self



class NotWritableMixin:
	"""Mix-in class which provides writing methods for non-writable file nodes.

	This class requires support for:
		* _checkNotClosed() method
	"""


	# The definition of those methods may seem odd
	# but it is the way Python (2.3) files work.

	def _notWritableError(self):
		"""_notWritableError() -> None

		Raises a common IOError exception for non-writable file nodes.
		"""
		raise IOError("the file is not writable")


	def truncate(self, size = None):
		"""truncate([size]) -> None.  Truncates the file node to at most 'size' bytes.

		Raises IOError.
		See file.truncate.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notWritableError()


	def write(self, string):
		"""write(string) -> None.  Writes the string to the file.

		Raises IOError.
		See file.write.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notWritableError()


	def writelines(self, sequence):
		"""writelines(sequence_of_strings) -> None.  Writes the strings to the file.

		Raises IOError.
		See file.writelines.__doc__ for more information.
		"""

		self._checkNotClosed()
		self._notWritableError()



class AppendableMixin:
	"""Mix-in class which provides writing methods for appendable file nodes.

	This class requires support for:
		* 'offset', 'node', '_vType' and '_vShape' attributes
		* _checkNotClosed() method
	"""

	def _appendZeros(self, size):
		"""_appendZeros(size) -> None.  Appends a string of zeros.

		Appends a string of 'size' zeros to the array,
		without moving the file pointer.
		"""

		# Appending an empty array would raise an error.
		if size == 0:
			return
		# XXX This may be redone to avoid a potentially large in-memory array.
		self.node.append(numpy.zeros(dtype=self._vType, shape=self._vShape(size)))


	def truncate(self, size = None):
		"""truncate([size]) -> None.  Truncates the file node to at most 'size' bytes.

		Currently, this method only makes sense to grow the file node,
		since data can not be rewritten nor deleted.
		See file.truncate.__doc__ for more information.
		"""

		self._checkNotClosed()

		if size is None:
			size = self.offset
		if size < self.node.nrows:
			raise IOError("truncating is only allowed for growing a file")
		self._appendZeros(size - self.node.nrows)


	def write(self, string):
		"""write(string) -> None.  Writes the string to the file.

		Writing an empty string does nothing, but requires the file to be open.
		See file.write.__doc__ for more information.
		"""

		self._checkNotClosed()

		# This mimics the behaviour of normal Python (2.3) files,
		# where writing an empty string does absolutely nothing
		# (not even moving the pointer of append-only files).
		if len(string) == 0:
			return

		# Is the pointer beyond the real end of data?
		end2off = self.offset - self.node.nrows
		if end2off > 0:
			# Zero-fill the gap between the end of data and the pointer.
			self._appendZeros(end2off)

		# Move the pointer to the end of the (newly written) data.
		self.offset = self.node.nrows

		# Append data.
		self.node.append(numpy.ndarray(buffer=string, dtype=self._vType,
									   shape = self._vShape(len(string))))

		# Move the pointer to the end of the written data.
		self.offset = self.node.nrows


	def writelines(self, sequence):
		"""writelines(sequence_of_strings) -> None.  Writes the strings to the file.

		See file.writelines.__doc__ for more information.
		"""

		for line in sequence:
			self.write(line)



class FileNode(object):
	"""FileNode() -> file node object

	Creates a new file node associated with a PyTables node,
	providing a standard Python file interface to it.

	This abstract class only provides attribute handling
	and file operations which do not depend on the file mode.

	The attribute set of the node becomes available via
	the 'attrs' property.
	You can add attributes there, but try to avoid
	attribute names in all caps or starting with '_',
	since they may clash with internal attributes.

	The node used as storage is also made available via
	the read-only attribute 'node'.
	Please do not tamper with this object unless unavoidably,
	since you may break the operation of the file node object.

	The constructor sets the 'closed' and 'softspace' attributes
	to their initial values, as well as the 'node' attribute to None.
	Sub-classes should set the 'node', 'mode', 'offset'
	and '_version' attributes,
	as well as define mode-dependent methods.

	Version 1 implements the file storage as an UInt8 Nx1 matrix EArray;
	version 2 uses an UInt8 N vector EArray.
	"""

	# The atom representing a byte in the array, for each version.
	_byteShape = [
		None,
		(0, 1),
		(0,)]

	# A lambda to turn a size into a shape, for each version.
	_sizeToShape = [
		None,
		lambda l: (l, 1),
		lambda l: (l,)]


	# The attribute set property methods.
	def getAttrs(self):
		"getAttrs() -> AttributeSet.  Gets the attribute set of the file node."

		return self.node.attrs

	def setAttrs(self, value):
		"setAttrs(string) -> None.  Raises ValueError."

		raise ValueError("changing the whole attribute set is not allowed")

	def delAttrs(self):
		"delAttrs() -> None.  Raises ValueError."

		raise ValueError("deleting the whole attribute set is not allowed")

	# The attribute set property.
	attrs = property(
		getAttrs, setAttrs, delAttrs,
		"A property pointing to the attribute set of the file node.")


	def __init__(self):
		super(FileNode, self).__init__()

		# The constructor of the subclass must set the value of
		# the instance attributes 'node', 'mode', 'offset' and '_version'.
		# It also has to set or check the node attributes.
		self.closed = False
		self.sofstpace = 0

		self.node   = None
		self.mode   = None
		self.offset = None
		self._version = None


	def __del__(self):
		if self.node is not None:
			self.close()


	def _setAttributes(self, node):
		"""_setAttributes(node) -> None.  Adds file node-specific attributes.

		Sets the system attributes 'NODE_TYPE' and 'NODE_TYPE_VERSION'
		in the specified PyTables node (leaf).
		"""

		attrs = node.attrs
		# System attributes are now writable.  ivb(2004-12-30)
		##attrs._g_setAttr('NODE_TYPE', NodeType)
		##attrs._g_setAttr('NODE_TYPE_VERSION', NodeTypeVersions[-1])
		attrs.NODE_TYPE         = NodeType
		attrs.NODE_TYPE_VERSION = NodeTypeVersions[-1]


	def _checkAttributes(self, node):
		"""_checkAttributes(node) -> None.  Checks file node-specific attributes.

		Checks for the presence and validity
		of the system attributes 'NODE_TYPE' and 'NODE_TYPE_VERSION'
		in the specified PyTables node (leaf).
		ValueError is raised if an attribute is missing or incorrect.
		"""

		attrs = node.attrs
		ltype    = getattr(attrs, 'NODE_TYPE', None)
		ltypever = getattr(attrs, 'NODE_TYPE_VERSION', None)

		if ltype != NodeType:
			raise ValueError("invalid type of node object: %s" % (ltype,))
		if ltypever not in NodeTypeVersions:
			raise ValueError(
				"unsupported type version of node object: %s" % (ltypever,))


	def _checkNotClosed(self):
		"""_checkNotClosed() -> None.  Checks if file node is open.

		Checks whether the file node is open or has been closed.
		In the second case, a ValueError is raised.
		If the host PyTables has been closed, ValueError is also raised.
		"""

		if self.closed:
			raise ValueError("I/O operation on closed file")
		if getattr(self.node, '_v_file', None) is None:
			raise ValueError("host PyTables file is already closed!")


	def close(self):
		"""close() -> None.  Closes the file node.

		Flushes the file and closes it.
		The 'node' attribute becomes None
		and the 'attrs' property becomes no longer available.
		See file.close.__doc__ for more information.
		"""

		# Only flush the first time the file is closed,
		# taking care of not doing it if the host PyTables file
		# has already been closed.
		if not self.closed:
			if getattr(self.node, '_v_file', None) is None:
				warnings.warn("host PyTables file is already closed!")
			else:
				self.flush()

		# Set the flag every time the method is called.
		self.closed = True
		# Release node object to allow closing the file.
		self.node = None


	def flush(self):
		"""flush() -> None.  Flushes the file node.

		See file.flush.__doc__ for more information.
		"""

		raise NotImplementedError


	def seek(self, offset, whence = 0):
		"""seek(offset[, whence]) -> None.  Moves to a new file position.

		See file.seek.__doc__ for more information.
		"""

		self._checkNotClosed()

		if whence == 0:
			newoffset = offset  # Absolute positioning.
		elif whence == 1:
			newoffset = self.offset + offset  # From pointer positioning.
		elif whence == 2:
			newoffset = self.node.nrows + offset  # From (real) end positioning.
		else:
			raise ValueError("invalid positioning mode")

		if newoffset < 0:
			# Positioning before the beginning is not allowed.
			raise IOError("can not seek before beginning of file")
		else:
			# Positioning beyond the end is allowed.
			self.offset = newoffset


	def tell(self):
		"""tell() -> long integer.  Gets the current file position.

		See file.tell.__doc__ for more information.
		"""

		self._checkNotClosed()
		return self.offset



class ROFileNode(ReadableMixin, NotWritableMixin, FileNode):
	"""ROFileNode(node) -> read-only file node object

	Creates a new read-only file node associated with the specified
	PyTables node, providing a standard Python file interface to it.
	The node has to have been created on a previous occasion
	using the newNode() function.

	This constructor is not intended to be used directly.
	Use the openNode() function instead.
	"""

	# Since FileNode provides all methods for read-only access,
	# only the constructor method and failing writing methods are needed.
	def __init__(self, node):
		super(ROFileNode, self).__init__()
		self._checkAttributes(node)

		self.node = node
		self.mode = 'r'
		self.offset = 0L
		self._version = node.attrs.NODE_TYPE_VERSION


	def __del__(self):
		super(ROFileNode, self).__del__()


	def flush(self):
		"""flush() -> None.  Flushes the file node.

		See file.flush.__doc__ for more information.
		"""

		self._checkNotClosed()
		# Do nothing.



class RAFileNode(ReadableMixin, AppendableMixin, FileNode):
	"""__init__(node, None), __init__(None, file, ...) -> writable file node object

	Creates a new read-write file node.
	The first syntax opens the specified PyTables node,
	while the second one creates a new node in the specified PyTables file.
	In the second case, additional named arguments 'where' and 'name'
	must be passed to specify where the file node is to be created.
	Other named arguments such as 'title' and 'filters' may also be passed.
	The special named argument 'expectedsize', indicating an estimate
	of the file size in bytes, may also be passed.

	Write access means reading as well as appending data is allowed.

	This constructor is not intended to be used directly.
	Use the newNode() or openNode() functions instead.
	"""

	__allowedInitKwArgs = ['where', 'name', 'title', 'filters', 'expectedsize']


	def __init__(self, node, h5file, **kwargs):
		super(RAFileNode, self).__init__()

		if node is not None:
			# Open an existing node and get its version.
			self._checkAttributes(node)
			self._version = node.attrs.NODE_TYPE_VERSION
		elif h5file is not None:
			# Check for allowed keyword arguments,
			# to avoid unwanted arguments falling through to array constructor.
			for kwarg in kwargs:
				if kwarg not in self.__allowedInitKwArgs:
					raise TypeError(
						"%s keyword argument is not allowed" % repr(kwarg))

			# Turn 'expectedsize' into 'expectedrows'.
			if 'expectedsize' in kwargs:
				# These match since one byte is stored per row.
				expectedrows = kwargs['expectedsize']
				kwargs = kwargs.copy()
				del kwargs['expectedsize']
				kwargs['expectedrows'] = expectedrows

			# Create a new array in the specified PyTables file.
			self._version = NodeTypeVersions[-1]
			shape = self._byteShape[self._version]
			node = h5file.createEArray(
				atom=tables.UInt8Atom(), shape=shape, **kwargs)

			# Set the node attributes, else remove the array itself.
			try:
				self._setAttributes(node)
			except RuntimeError:
				h5file.removeNode(kwargs['where'], kwargs['name'])
				raise

		# Set required attributes (besides of '_version').
		self.node = node
		self.mode = 'a+'
		self.offset = 0L

		# Cache some dictionary lookups regarding file version.
		# self._version is a NumPy scalar and when Python < 2.5
		# this cannot be used as an index.
		# Will force a conversion to an integer.
		version = int(self._version)
		self._vType = tables.UInt8Atom().dtype.base.type
		self._vShape = self._sizeToShape[version]


	def __del__(self):
		super(RAFileNode, self).__del__()


	def flush(self):
		"""flush() -> None.  Flushes the file node.

		See file.flush.__doc__ for more information.
		"""

		self._checkNotClosed()
		self.node.flush()



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