Author: bugman
Date: Fri Sep 26 19:36:39 2014
New Revision: 26082
URL: http://svn.gna.org/viewcvs/relax?rev=26082&view=rev
Log:
Merged revisions 26071-26072 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26071 | bugman | 2014-09-26 18:29:26 +0200 (Fri, 26 Sep 2014) | 10 lines
Fix for the cdp.exp_info.software data structure setup.
This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the
corrupted relax state files
after setting the relax references via the bmrb.software, bmrb.display, or
bmrb.write user
functions.
The Element data container name was being replaced by the software name,
making it impossible to
restore from the XML.
........
r26072 | bugman | 2014-09-26 18:43:09 +0200 (Fri, 26 Sep 2014) | 10 lines
Implemented the cdp.exp_info.from_xml() method to correctly restore the
experimental info structure.
This fixes bug #22704 (https://gna.org/bugs/?22704), the corrupted relax
state files after setting
the relax references via the bmrb.software, bmrb.display, or bmrb.write
user functions.
This custom ExpInfo.from_xml() method is required to properly recreate the
software, script and
citation list data structures of the cdp.exp_info data structure, as these
are special RelaxListType
objects populated by Element objects (both from data_store.data_classes).
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/data_store/exp_info.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Sep 26 19:36:39 2014
@@ -1 +1 @@
-/trunk:1-26017,26043-26070
+/trunk:1-26017,26043-26072
Modified: branches/frame_order_cleanup/data_store/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/data_store/exp_info.py?rev=26082&r1=26081&r2=26082&view=diff
==============================================================================
--- branches/frame_order_cleanup/data_store/exp_info.py (original)
+++ branches/frame_order_cleanup/data_store/exp_info.py Fri Sep 26 19:36:39
2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2009-2013 Edward d'Auvergne
#
+# Copyright (C) 2009-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -24,6 +24,7 @@
# relax module imports.
from data_store.data_classes import RelaxListType, Element
+from lib.xml import xml_to_object
class ExpInfo(Element):
@@ -118,6 +119,44 @@
self.citations.append(cite)
+ def from_xml(self, exp_info_node, file_version=1):
+ """Recreate the element data structure from the XML element node.
+
+ @param super_node: The element XML node.
+ @type super_node: xml.dom.minicompat.Element instance
+ @keyword file_version: The relax XML version of the XML file.
+ @type file_version: int
+ """
+
+ # Recreate the list structures.
+ list_node_names = ['citation_list', 'script_list', 'software_list']
+ list_subnode_names = ['citation', 'script', 'software']
+ list_str_names = ['citations', 'scripts', 'software']
+ for i in range(len(list_node_names)):
+ # Get the list node.
+ list_node =
exp_info_node.getElementsByTagName(list_node_names[i])
+
+ # Necreate the structure, if the node exists.
+ if list_node:
+ # Initialise the data structure.
+ setattr(self, list_str_names[i], RelaxListType())
+ list_obj = getattr(self, list_str_names[i])
+
+ # Get all the subnodes.
+ list_nodes =
list_node[0].getElementsByTagName(list_subnode_names[i])
+
+ # Loop over the nodes.
+ for node in list_nodes:
+ # Add a blank container.
+ list_obj.append(Element(name=node.tagName,
desc=node.getAttribute('desc')))
+
+ # Recreate the element.
+ list_obj[-1].from_xml(node, file_version=file_version)
+
+ # Recreate all the other data structures.
+ xml_to_object(exp_info_node, self, file_version=file_version,
blacklist=list_node_names)
+
+
def get_cite_id_num(self, cite_id):
"""Return the citation ID number for the given citation ID string.
@@ -258,7 +297,7 @@
software.desc = "Software program used in the analysis"
# Set the attributes.
- software.name = name
+ software.software_name = name
software.url = url
software.version = version
software.vendor_name = vendor_name
r26082 - in /branches/frame_order_cleanup: ./ data_store/exp_info.py