Author: bugman
Date: Sun Jun 22 16:50:03 2008
New Revision: 6414
URL: http://svn.gna.org/viewcvs/relax?rev=6414&view=rev
Log:
Shifted and renamed the XML module.
Added:
1.3/data/relax_xml.py
- copied unchanged from r6413, 1.3/generic_fns/xml_data_pipe.py
Removed:
1.3/generic_fns/xml_data_pipe.py
Removed: 1.3/generic_fns/xml_data_pipe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/xml_data_pipe.py?rev=6413&view=auto
==============================================================================
--- 1.3/generic_fns/xml_data_pipe.py (original)
+++ 1.3/generic_fns/xml_data_pipe.py (removed)
@@ -1,188 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module for the creation and parsing of an XML representation of a data
pipe."""
-
-# Python module imports.
-from re import search
-
-# relax module imports.
-from data import Relax_data_store; ds = Relax_data_store()
-from version import version
-
-
-def create_diff_elem(doc, elem):
- """Create an XML element for the diffusion tensor.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @param elem: The element to add the diffusion tensor element to.
- @type elem: XML element object
- """
-
- # Create the diffusion tensor element and add it to the higher level
element.
- tensor_elem = doc.createElement('diff_tensor')
- elem.appendChild(tensor_elem)
-
- # Set the diffusion tensor attributes.
- tensor_elem.setAttribute('desc', 'Diffusion tensor')
- tensor_elem.setAttribute('type', ds[ds.current_pipe].diff_tensor.type)
-
- # Add all simple python objects within the PipeContainer to the pipe
element.
- fill_object_contents(doc, tensor_elem,
object=ds[ds.current_pipe].diff_tensor, blacklist=['is_empty', 'type'])
-
-
-def create_hybrid_elem(doc, elem):
- """Create an XML element for the data pipe hybridisation information.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @param elem: The element to add the hybridisation info to.
- @type elem: XML element object
- """
-
- # Create the hybrid element and add it to the higher level element.
- hybrid_elem = doc.createElement('hybrid')
- elem.appendChild(hybrid_elem)
-
- # Set the hybridisation attributes.
- hybrid_elem.setAttribute('desc', 'Data pipe hybridisation information')
-
- # Create an element to store the pipes list.
- list_elem = doc.createElement('pipes')
- hybrid_elem.appendChild(list_elem)
-
- # Add the pipes list.
- text_val = doc.createTextNode(str(ds[ds.current_pipe].hybrid_pipes))
- list_elem.appendChild(text_val)
-
-
-def create_pipe_elem(doc, elem):
- """Create an XML element for the data pipe, and add data pipe info as
attributes.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @param elem: The element to add the pipe element to.
- @type elem: XML element object
- @return: The data pipe element.
- @rtype: XML element object
- """
-
- # Create the pipe element and add it to the higher level element.
- pipe_elem = doc.createElement('pipe')
- elem.appendChild(pipe_elem)
-
- # Set the data pipe attributes.
- pipe_elem.setAttribute('desc', 'The contents of a relax data pipe')
- pipe_elem.setAttribute('name', ds.current_pipe)
- pipe_elem.setAttribute('type', ds[ds.current_pipe].pipe_type)
-
- # Return the pipe element.
- return pipe_elem
-
-
-def create_str_elem(doc, elem):
- """Create an XML element for the structural information.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @param elem: The element to add the structural info to.
- @type elem: XML element object
- """
-
- # Create the structural element and add it to the higher level element.
- str_elem = doc.createElement('structure')
- elem.appendChild(str_elem)
-
- # Set the structural attributes.
- str_elem.setAttribute('desc', 'Structural information')
- str_elem.setAttribute('id', ds[ds.current_pipe].structure.id)
-
-
-def create_top_level(doc):
- """Create the top level XML element including all the information needed
about relax.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @return: The top level relax element.
- @rtype: XML element object
- """
-
- # Create the element, including the relax URL.
- top_elem = doc.createElementNS('http://nmr-relax.com', 'relax')
-
- # Append the element.
- doc.appendChild(top_elem)
-
- # Set the relax version number.
- top_elem.setAttribute('version', version)
-
- # Return the element.
- return top_elem
-
-
-def fill_object_contents(doc, elem, object=None, blacklist=None):
- """Place all simple python objects into the XML element namespace.
-
- @param doc: The XML document object.
- @type doc: xml.dom.minidom.Document instance
- @param elem: The element to add all python objects to.
- @type elem: XML element object
- @param object: The python class instance containing the objects to
add.
- @type object: instance
- @param blacklist: A list of object names to exclude.
- @type blacklist: list of str
- """
-
- # Loop over the elements of the object.
- for name in dir(object):
- # Skip blacklisted objects.
- if name in blacklist:
- continue
-
- # Skip special objects.
- if search("^_", name):
- continue
-
- # Only pack objects in the __mod_attr__ list, if that list exists.
- if hasattr(object, '__mod_attr__') and name not in
object.__mod_attr__:
- continue
-
- # Create a new element for this object, and add it to the main
element.
- sub_elem = doc.createElement(name)
- elem.appendChild(sub_elem)
-
- # Add the text value to the sub element.
- text_val = doc.createTextNode(`getattr(object, name)`)
- sub_elem.appendChild(text_val)
-
-
-def read(file, verbosity=1):
- """Parse a XML document representation of a data pipe, and load it into
the relax data store.
-
- @param file: The open file object.
- @type file: file
- @keyword verbosity: A flag specifying the amount of information to
print. The higher the value,
- the greater the verbosity.
- @type verbosity: int
- """
r6414 - in /1.3: data/relax_xml.py generic_fns/xml_data_pipe.py