Author: bugman
Date: Fri Sep 11 11:12:30 2009
New Revision: 9511
URL: http://svn.gna.org/viewcvs/relax?rev=9511&view=rev
Log:
Updated the relax data store from_xml() method for support of the loading of
the XML state file.
Modified:
1.3/data/__init__.py
1.3/generic_fns/results.py
Modified: 1.3/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/__init__.py?rev=9511&r1=9510&r2=9511&view=diff
==============================================================================
--- 1.3/data/__init__.py (original)
+++ 1.3/data/__init__.py Fri Sep 11 11:12:30 2009
@@ -28,12 +28,14 @@
import __builtin__
from re import search
from string import split
+from sys import stderr
from time import asctime
import xml.dom.minidom
# relax module imports.
from pipe_container import PipeContainer
-from relax_errors import RelaxPipeError
+import generic_fns
+from relax_errors import RelaxError, RelaxPipeError, RelaxNoPipeError
from version import version
@@ -175,6 +177,7 @@
# No pipes should exist.
if not self.keys() == []:
+ stderr.write("The relax data store contains the data pipes
%s.\n" % self.keys())
return False
# An object has been added to the data store.
@@ -192,22 +195,36 @@
continue
# An object has been added.
+ stderr.write("The relax data store contains the object %s.\n" %
name)
return False
# The data store is empty.
return True
- def from_xml(self, file, dir=None, verbosity=1):
+ def from_xml(self, file, dir=None, pipe_to=None, 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 dir: The name of the directory containing the results
file.
- @type dir: str
- @keyword verbosity: A flag specifying the amount of information to
print. The higher the value,
- the greater the verbosity.
- @type verbosity: int
+ @param file: The open file object.
+ @type file: file
+ @keyword dir: The name of the directory containing the
results file (needed
+ for loading external files).
+ @type dir: str
+ @keyword pipe_to: The data pipe to load the XML data pipe
into (the file must only
+ contain one data pipe).
+ @type pipe_to: str
+ @keyword verbosity: A flag specifying the amount of
information to print. The
+ higher the value, the greater the
verbosity.
+ @type verbosity: int
+ @raises RelaxError: If pipe_to is given and the file
contains multiple pipe
+ elements; or if the data pipes in the
XML file already exist in
+ the relax data store; or if the data
pipe type is invalid; or
+ if the target data pipe is not empty.
+ @raises RelaxNoPipeError: If pipe_to is given but the data pipe
does not exist.
+ @raises RelaxError: If the data pipes in the XML file
already exist in the relax
+ data store, or if the data pipe type is
invalid.
+ @raises RelaxPipeError: If the data pipes of the XML file are
already present in the
+ relax data store.
"""
# Create the XML document from the file.
@@ -219,8 +236,60 @@
# Get the relax version of the XML file.
relax_version = str(relax_node.getAttribute('version'))
- # Fill the pipe.
- self[self.instance.current_pipe].from_xml(relax_node, dir=dir)
+ # Get the pipe nodes.
+ pipe_nodes = relax_node.getElementsByTagName('pipe')
+
+ # Target loading to a specific pipe (for pipe results reading).
+ if pipe_to:
+ # Check if there are multiple pipes in the XML file.
+ if len(pipe_nodes) > 1:
+ raise RelaxError("The pipe_to target pipe argument '%s'
cannot be given as the file contains multiple pipe elements." % pipe_to)
+
+ # The pipe type.
+ pipe_type = pipe_nodes[0].getAttribute('type')
+
+ # Check that the pipe already exists.
+ if not pipe_to in self:
+ raise RelaxNoPipeError(pipe_to)
+
+ # Check if the pipe type matches.
+ if pipe_type != self[pipe_to].pipe_type:
+ raise RelaxError("The XML file pipe type '%s' does not match
the pipe type '%s'" % (pipe_type, self[pipe_to].pipe_type))
+
+ # Check if the pipe is empty.
+ if not self[pipe_to].is_empty():
+ raise RelaxError("The data pipe '%s' is not empty." %
pipe_to)
+
+ # Load the data.
+ self[pipe_to].from_xml(pipe_nodes[0], dir=dir)
+
+ # Load the state.
+ else:
+ # Checks.
+ for pipe_node in pipe_nodes:
+ # The pipe name and type.
+ pipe_name = pipe_node.getAttribute('name')
+ pipe_type = pipe_node.getAttribute('type')
+
+ # Existence check.
+ if pipe_name in self:
+ raise RelaxPipeError(pipe_name)
+
+ # Valid type check.
+ if not pipe_type in generic_fns.pipes.VALID_TYPES:
+ raise RelaxError("The data pipe type '%s' is invalid and
must be one of the strings in the list %s." % (pipe_type,
generic_fns.pipes.VALID_TYPES))
+
+ # Load the data pipes.
+ for pipe_node in pipe_nodes:
+ # The pipe name and type.
+ pipe_name = pipe_node.getAttribute('name')
+ pipe_type = pipe_node.getAttribute('type')
+
+ # Add the data pipe.
+ self.add(pipe_name, pipe_type)
+
+ # Fill the pipe.
+ self[pipe_name].from_xml(pipe_node, dir=dir)
def to_xml(self, file, pipes=None):
Modified: 1.3/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/results.py?rev=9511&r1=9510&r2=9511&view=diff
==============================================================================
--- 1.3/generic_fns/results.py (original)
+++ 1.3/generic_fns/results.py Fri Sep 11 11:12:30 2009
@@ -93,7 +93,7 @@
# XML results.
if format == 'xml':
- read_function = ds.from_xml(file, dir=dirname(file_path))
+ ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name())
# Columnar results.
elif format == 'columnar':
r9511 - in /1.3: data/__init__.py generic_fns/results.py