def to_xml(self, doc, element):
"""Create XML elements for each model.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the model XML elements to.
@type element: XML element object
"""
# Loop over the models.
for i in range(len(self)):
# Create an XML element for this model and add it to the higher level element.
model_element = doc.createElement('model')
element.appendChild(model_element)
# Set the model attributes.
model_element.setAttribute('desc', 'Model container')
model_element.setAttribute('num', str(self[i].num))
# Add all simple python objects within the ModelContainer to the XML element.
fill_object_contents(doc,
model_element,
object=self[i],
blacklist=['num', 'mol'] +
list(self[i].__class__.__dict__.keys()))
# Add the molecule data.
self[i].mol.to_xml(doc, model_element)
def to_xml(self, doc, element):
"""Create an XML element for the alignment tensors.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the alignment tensors XML element to.
@type element: XML element object
"""
# Create the alignment tensors element and add it to the higher level element.
tensor_list_element = doc.createElement('align_tensors')
element.appendChild(tensor_list_element)
# Set the alignment tensor attributes.
tensor_list_element.setAttribute('desc', 'Alignment tensor list')
# Add all simple python objects within the PipeContainer to the pipe element.
fill_object_contents(doc, tensor_list_element, object=self, blacklist=list(self.__class__.__dict__.keys())+list(list.__dict__.keys()))
# Loop over the tensors.
for i in range(len(self)):
# Create an XML element for a single tensor.
tensor_element = doc.createElement('align_tensor')
tensor_list_element.appendChild(tensor_element)
tensor_element.setAttribute('index', repr(i))
tensor_element.setAttribute('desc', 'Alignment tensor')
# The blacklist.
blacklist = ['type', 'is_empty'] + list(self[i].__class__.__dict__.keys())
for name in dir(self):
if name not in self[i]._mod_attr:
blacklist.append(name)
# Add all simple python objects within the PipeContainer to the pipe element.
fill_object_contents(doc, tensor_element, object=self[i], blacklist=blacklist)
def to_xml(self, doc, element):
"""Create an XML element for the diffusion tensor.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the diffusion tensor element to.
@type element: XML element object
"""
# Create the diffusion tensor element and add it to the higher level element.
tensor_element = doc.createElement('diff_tensor')
element.appendChild(tensor_element)
# Set the diffusion tensor attributes.
tensor_element.setAttribute('desc', 'Diffusion tensor')
tensor_element.setAttribute('type', self.type)
# The blacklist.
blacklist = ['type', 'is_empty'] + list(self.__class__.__dict__.keys())
for name in dir(self):
if name not in self._mod_attr:
blacklist.append(name)
# Add all simple python objects within the PipeContainer to the pipe element.
fill_object_contents(doc, tensor_element, object=self, blacklist=blacklist)
def to_xml(self, doc, element, pipe_type=None):
"""Create XML elements for each molecule.
@param doc: The XML document object.
@type doc: Xml.dom.minidom.Document instance
@param element: The element to add the molecule XML elements to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# Loop over the molecules.
for i in range(len(self)):
# Create an XML element for this molecule and add it to the higher level element.
mol_element = doc.createElement('mol')
element.appendChild(mol_element)
# Set the molecule attributes.
mol_element.setAttribute('desc', 'Molecule container')
mol_element.setAttribute('name', str(self[i].name))
mol_element.setAttribute('type', str(self[i].type))
# Add all simple python objects within the MoleculeContainer to the XML element.
fill_object_contents(doc,
mol_element,
object=self[i],
blacklist=['name', 'res', 'type'] +
list(self[i].__class__.__dict__.keys()))
# Add the residue data.
self[i].res.to_xml(doc, mol_element, pipe_type=pipe_type)
def to_xml(self, doc, element, pipe_type=None):
"""Create XML elements for each molecule.
@param doc: The XML document object.
@type doc: Xml.dom.minidom.Document instance
@param element: The element to add the molecule XML elements to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# Loop over the molecules.
for i in range(len(self)):
# Create an XML element for this molecule and add it to the higher level element.
mol_element = doc.createElement('mol')
element.appendChild(mol_element)
# Set the molecule attributes.
mol_element.setAttribute('desc', 'Molecule container')
mol_element.setAttribute('name', str(self[i].name))
mol_element.setAttribute('type', str(self[i].type))
# Add all simple python objects within the MoleculeContainer to the XML element.
fill_object_contents(doc, mol_element, object=self[i], blacklist=['name', 'res', 'type'] + list(self[i].__class__.__dict__.keys()))
# Add the residue data.
self[i].res.to_xml(doc, mol_element, pipe_type=pipe_type)
def to_xml(self, doc, element):
"""Create an XML element for the diffusion tensor.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the diffusion tensor element to.
@type element: XML element object
"""
# Create the diffusion tensor element and add it to the higher level element.
tensor_element = doc.createElement('diff_tensor')
element.appendChild(tensor_element)
# Set the diffusion tensor attributes.
tensor_element.setAttribute('desc', 'Diffusion tensor')
tensor_element.setAttribute('type', self.type)
# The blacklist.
blacklist = ['type', 'is_empty'] + list(self.__class__.__dict__.keys())
for name in dir(self):
if name not in self._mod_attr:
blacklist.append(name)
# Add all simple python objects within the PipeContainer to the pipe element.
fill_object_contents(doc,
tensor_element,
object=self,
blacklist=blacklist)
def to_xml(self, doc, element):
"""Create an XML element for the list data structure.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the list data structure XML element to.
@type element: XML element object
"""
# Create the element and add it to the higher level element.
list_element = doc.createElement(self.list_name)
element.appendChild(list_element)
# Set the list attributes.
list_element.setAttribute('desc', self.list_desc)
# Blacklisted objects.
blacklist = ['list_name', 'list_desc', 'element_name', 'element_desc', 'blacklist'] + list(self.__dict__.keys()) + list(RelaxListType.__dict__.keys()) + list(self.__class__.__dict__.keys()) + list(list.__dict__.keys()) + list(list.__dict__.keys())
# Add all simple python objects within the list to the list element.
fill_object_contents(doc, list_element, object=self, blacklist=blacklist)
# Loop over the list.
for i in range(len(self)):
# The element has its own to_xml() method.
if hasattr(self[i], 'to_xml'):
self[i].to_xml(doc, list_element)
# Normal element.
else:
# Create an XML element for each container.
list_item_element = doc.createElement(self.element_name)
list_element.appendChild(list_item_element)
list_item_element.setAttribute('index', repr(i))
list_item_element.setAttribute('desc', self.element_desc)
# Blacklisted objects.
blacklist = list(self[i].__class__.__dict__.keys())
# Add objects which have to_xml() methods.
for name in dir(self[i]):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self[i], name)
if hasattr(obj, 'to_xml'):
obj.to_xml(doc, list_item_element)
blacklist = blacklist + [name]
# Add all simple python objects within the container to the XML element.
fill_object_contents(doc, list_item_element, object=self[i], blacklist=blacklist)
def to_xml(self, doc, element):
"""Create an XML element for the list data structure.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the list data structure XML element to.
@type element: XML element object
"""
# Create the element and add it to the higher level element.
list_element = doc.createElement(self.list_name)
element.appendChild(list_element)
# Set the list attributes.
list_element.setAttribute('desc', self.list_desc)
# Blacklisted objects.
blacklist = ['list_name', 'list_desc', 'element_name', 'element_desc', 'blacklist'] + list(self.__dict__.keys()) + list(RelaxListType.__dict__.keys()) + list(self.__class__.__dict__.keys()) + list(list.__dict__.keys()) + list(list.__dict__.keys())
# Add all simple python objects within the list to the list element.
fill_object_contents(doc, list_element, object=self, blacklist=blacklist)
# Loop over the list.
for i in range(len(self)):
# The element has its own to_xml() method.
if hasattr(self[i], 'to_xml'):
self[i].to_xml(doc, list_element)
# Normal element.
else:
# Create an XML element for each container.
list_item_element = doc.createElement(self.element_name)
list_element.appendChild(list_item_element)
list_item_element.setAttribute('index', repr(i))
list_item_element.setAttribute('desc', self.element_desc)
# Blacklisted objects.
blacklist = list(self[i].__class__.__dict__.keys())
# Add objects which have to_xml() methods.
for name in dir(self[i]):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self[i], name)
if hasattr(obj, 'to_xml'):
obj.to_xml(doc, list_item_element)
blacklist = blacklist + [name]
# Add all simple python objects within the container to the XML element.
fill_object_contents(doc, list_item_element, object=self[i], blacklist=blacklist)
def to_xml(self, doc, element, pipe_type=None):
"""Create a XML element for the current data pipe.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The XML element to add the pipe XML element to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# Add all simple python objects within the PipeContainer to the global element.
global_element = doc.createElement('global')
element.appendChild(global_element)
global_element.setAttribute(
'desc', 'Global data located in the top level of the data pipe')
fill_object_contents(
doc,
global_element,
object=self,
blacklist=[
'align_tensors', 'diff_tensor', 'exp_info', 'interatomic',
'hybrid_pipes', 'mol', 'pipe_type', 'structure'
] + list(self.__class__.__dict__.keys()))
# Hybrid info.
self.xml_create_hybrid_element(doc, element)
# Add the experimental information.
if hasattr(self, 'exp_info'):
self.exp_info.to_xml(doc, element)
# Add the diffusion tensor data.
if hasattr(self, 'diff_tensor'):
self.diff_tensor.to_xml(doc, element)
# Add the alignment tensor data.
if hasattr(self, 'align_tensors'):
self.align_tensors.to_xml(doc, element)
# Add the molecule-residue-spin data.
self.mol.to_xml(doc, element, pipe_type=pipe_type)
# Add the interatomic data.
self.interatomic.to_xml(doc, element, pipe_type=pipe_type)
# Add the structural data, if it exists.
if hasattr(self, 'structure'):
self.structure.to_xml(doc, element)
def to_xml(self, doc, element):
"""Create an XML element for the alignment tensors.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the alignment tensors XML element to.
@type element: XML element object
"""
# Create the alignment tensors element and add it to the higher level element.
tensor_list_element = doc.createElement('align_tensors')
element.appendChild(tensor_list_element)
# Set the alignment tensor attributes.
tensor_list_element.setAttribute('desc', 'Alignment tensor list')
# Add all simple python objects within the PipeContainer to the pipe element.
fill_object_contents(doc,
tensor_list_element,
object=self,
blacklist=list(self.__class__.__dict__.keys()) +
list(list.__dict__.keys()))
# Loop over the tensors.
for i in range(len(self)):
# Create an XML element for a single tensor.
tensor_element = doc.createElement('align_tensor')
tensor_list_element.appendChild(tensor_element)
tensor_element.setAttribute('index', repr(i))
tensor_element.setAttribute('desc', 'Alignment tensor')
# The blacklist.
blacklist = ['type', 'is_empty'] + list(
self[i].__class__.__dict__.keys())
for name in dir(self):
if name not in self[i]._mod_attr:
blacklist.append(name)
# Add all simple python objects within the PipeContainer to the pipe element.
fill_object_contents(doc,
tensor_element,
object=self[i],
blacklist=blacklist)
def to_xml(self, doc, element):
"""Create XML elements for the contents of this molecule container.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the molecule XML elements to.
@type element: XML element object
"""
# Create an XML element for this molecule and add it to the higher level element.
mol_element = doc.createElement('mol_cont')
element.appendChild(mol_element)
# Set the molecule attributes.
mol_element.setAttribute('desc', 'Molecule container')
mol_element.setAttribute('name', str(self.mol_name))
# Add all simple python objects within the MolContainer to the XML element.
fill_object_contents(doc, mol_element, object=self, blacklist=list(self.__class__.__dict__.keys()))
def to_xml(self, doc, element):
"""Create an XML element for the container.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the data container XML element to.
@type element: XML element object
"""
# Create a new element for this container and add it to the higher level element.
cont_element = doc.createElement(self.name)
element.appendChild(cont_element)
# Set the list attributes.
cont_element.setAttribute('desc', self.desc)
# Blacklisted objects.
blacklist = self.blacklist + ['name', 'desc', 'blacklist'] + list(Element.__dict__.keys()) + list(self.__class__.__dict__.keys()) + list(object.__dict__.keys())
# Store and blacklist the objects which have to_xml() methods.
to_xml_list = []
for name in dir(self):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self, name)
if hasattr(obj, 'to_xml'):
to_xml_list.append(obj)
blacklist = blacklist + [name]
# Add all simple python objects within the container to the XML element.
fill_object_contents(doc, cont_element, object=self, blacklist=blacklist)
# Execute the object to_xml() methods.
for obj in to_xml_list:
obj.to_xml(doc, cont_element)
def to_xml(self, doc, element):
"""Create an XML element for the container.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the data container XML element to.
@type element: XML element object
"""
# Create a new element for this container and add it to the higher level element.
cont_element = doc.createElement(self.name)
element.appendChild(cont_element)
# Set the list attributes.
cont_element.setAttribute('desc', self.desc)
# Blacklisted objects.
blacklist = self.blacklist + ['name', 'desc', 'blacklist'] + list(Element.__dict__.keys()) + list(self.__class__.__dict__.keys()) + list(object.__dict__.keys())
# Store and blacklist the objects which have to_xml() methods.
to_xml_list = []
for name in dir(self):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self, name)
if hasattr(obj, 'to_xml'):
to_xml_list.append(obj)
blacklist = blacklist + [name]
# Add all simple python objects within the container to the XML element.
fill_object_contents(doc, cont_element, object=self, blacklist=blacklist)
# Execute the object to_xml() methods.
for obj in to_xml_list:
obj.to_xml(doc, cont_element)
def to_xml(self, doc, element, pipe_type=None):
"""Create a XML element for the current data pipe.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The XML element to add the pipe XML element to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# Add all simple python objects within the PipeContainer to the global element.
global_element = doc.createElement('global')
element.appendChild(global_element)
global_element.setAttribute('desc', 'Global data located in the top level of the data pipe')
fill_object_contents(doc, global_element, object=self, blacklist=['align_tensors', 'diff_tensor', 'exp_info', 'interatomic', 'hybrid_pipes', 'mol', 'pipe_type', 'structure'] + list(self.__class__.__dict__.keys()))
# Hybrid info.
self.xml_create_hybrid_element(doc, element)
# Add the experimental information.
if hasattr(self, 'exp_info'):
self.exp_info.to_xml(doc, element)
# Add the diffusion tensor data.
if hasattr(self, 'diff_tensor'):
self.diff_tensor.to_xml(doc, element)
# Add the alignment tensor data.
if hasattr(self, 'align_tensors'):
self.align_tensors.to_xml(doc, element)
# Add the molecule-residue-spin data.
self.mol.to_xml(doc, element, pipe_type=pipe_type)
# Add the interatomic data.
self.interatomic.to_xml(doc, element, pipe_type=pipe_type)
# Add the structural data, if it exists.
if hasattr(self, 'structure'):
self.structure.to_xml(doc, element)
def to_xml(self, doc, element):
"""Create XML elements for the contents of this molecule container.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the molecule XML elements to.
@type element: XML element object
"""
# Create an XML element for this molecule and add it to the higher level element.
mol_element = doc.createElement('mol_cont')
element.appendChild(mol_element)
# Set the molecule attributes.
mol_element.setAttribute('desc', 'Molecule container')
mol_element.setAttribute('name', str(self.mol_name))
# Add all simple python objects within the MolContainer to the XML element.
fill_object_contents(doc,
mol_element,
object=self,
blacklist=list(self.__class__.__dict__.keys()))
def to_xml(self, doc, element):
"""Create XML elements for each model.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the model XML elements to.
@type element: XML element object
"""
# Loop over the models.
for i in range(len(self)):
# Create an XML element for this model and add it to the higher level element.
model_element = doc.createElement('model')
element.appendChild(model_element)
# Set the model attributes.
model_element.setAttribute('desc', 'Model container')
model_element.setAttribute('num', str(self[i].num))
# Add all simple python objects within the ModelContainer to the XML element.
fill_object_contents(doc, model_element, object=self[i], blacklist=['num', 'mol'] + list(self[i].__class__.__dict__.keys()))
# Add the molecule data.
self[i].mol.to_xml(doc, model_element)
def to_xml(self, doc, element, pipe_type=None):
"""Create XML elements for each spin.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the spin XML elements to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# The specific analysis API object.
api = specific_analyses.api.return_api(analysis_type=pipe_type)
# Loop over the containers.
for i in range(len(self)):
# Create an XML element for this container and add it to the higher level element.
interatom_element = doc.createElement('interatomic')
element.appendChild(interatom_element)
# Set the spin attributes.
interatom_element.setAttribute('desc',
'Interatomic data container')
interatom_element.setAttribute('spin_id1', str(self[i].spin_id1))
interatom_element.setAttribute('spin_id2', str(self[i].spin_id2))
# Get the specific object names and loop over them to get their descriptions.
object_info = []
try:
for name in api.data_names(error_names=True, sim_names=True):
# Get the description.
if hasattr(api, 'return_data_desc'):
desc = api.return_data_desc(name)
else:
desc = None
# Append the two.
object_info.append([name, desc])
except RelaxImplementError:
pass
# Add the ordered objects.
blacklist = []
for name, desc in object_info:
# Add the name to the blacklist.
blacklist.append(name)
# Skip the object if it is missing from the InteratomContainer.
if not hasattr(self[i], name):
continue
# Create a new element for this object, and add it to the main element.
sub_element = doc.createElement(name)
interatom_element.appendChild(sub_element)
# Add the object description.
if desc:
sub_element.setAttribute('desc', desc)
# Get the object.
object = getattr(self[i], name)
# Convert to XML.
object_to_xml(doc, sub_element, value=object)
# Add all simple python objects within the InteratomContainer to the XML element.
fill_object_contents(doc,
interatom_element,
object=self[i],
blacklist=['spin_id1', 'spin_id2'] +
blacklist +
list(self[i].__class__.__dict__.keys()))
def to_xml(self, file, pipes=None):
"""Create a XML document representation of the current data pipe.
This method creates the top level XML document including all the information needed
about relax, calls the PipeContainer.xml_write() method to fill in the document contents,
and writes the XML into the file object.
@param file: The open file object.
@type file: file
@param pipes: The name of the pipe, or list of pipes to place in the XML file.
@type pipes: str or list of str
"""
# The pipes to include in the XML file.
all = False
if not pipes:
all = True
pipes = list(self.keys())
elif isinstance(pipes, str):
pipes = [pipes]
# Sort the pipes.
pipes.sort()
# Create the XML document object.
xmldoc = xml.dom.minidom.Document()
# Create the top level element, including the relax URL.
top_element = xmldoc.createElementNS('http://www.nmr-relax.com',
'relax')
top_element.setAttribute("xmlns", "http://www.nmr-relax.com")
# Append the element.
xmldoc.appendChild(top_element)
# Set the relax version number, and add a creation time.
top_element.setAttribute('version', version.version)
top_element.setAttribute('time', asctime())
top_element.setAttribute('file_version', "2")
if version.repo_head:
top_element.setAttribute('head', version.repo_head)
if version.repo_url:
top_element.setAttribute('url',
version.repo_url.replace('\n', '; '))
# Add all objects in the data store base object to the XML element.
if all:
blacklist = list(self.__class__.__dict__.keys()) + list(
dict.__dict__.keys())
for name in dir(self):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self, name)
if hasattr(obj, 'to_xml'):
obj.to_xml(xmldoc, top_element)
blacklist = blacklist + [name]
# Remove the current data pipe from the blacklist!
blacklist.remove('current_pipe')
# Add all simple python objects within the store.
fill_object_contents(xmldoc,
top_element,
object=self,
blacklist=blacklist)
# Loop over the pipes.
for pipe in pipes:
# Create the pipe XML element and add it to the top level XML element.
pipe_element = xmldoc.createElement('pipe')
top_element.appendChild(pipe_element)
# Set the data pipe attributes.
pipe_element.setAttribute('desc',
'The contents of a relax data pipe')
pipe_element.setAttribute('name', pipe)
pipe_element.setAttribute('type', self[pipe].pipe_type)
# Fill the data pipe XML element.
self[pipe].to_xml(xmldoc,
pipe_element,
pipe_type=self[pipe].pipe_type)
# Write out the XML file.
file.write(xmldoc.toprettyxml(indent=' '))
def to_xml(self, file, pipes=None):
"""Create a XML document representation of the current data pipe.
This method creates the top level XML document including all the information needed
about relax, calls the PipeContainer.xml_write() method to fill in the document contents,
and writes the XML into the file object.
@param file: The open file object.
@type file: file
@param pipes: The name of the pipe, or list of pipes to place in the XML file.
@type pipes: str or list of str
"""
# The pipes to include in the XML file.
all = False
if not pipes:
all = True
pipes = list(self.keys())
elif isinstance(pipes, str):
pipes = [pipes]
# Sort the pipes.
pipes.sort()
# Create the XML document object.
xmldoc = xml.dom.minidom.Document()
# Create the top level element, including the relax URL.
top_element = xmldoc.createElementNS('http://www.nmr-relax.com', 'relax')
top_element.setAttribute("xmlns", "http://www.nmr-relax.com")
# Append the element.
xmldoc.appendChild(top_element)
# Set the relax version number, and add a creation time.
top_element.setAttribute('version', version.version)
top_element.setAttribute('time', asctime())
top_element.setAttribute('file_version', "2")
if version.repo_revision:
top_element.setAttribute('revision', version.repo_revision)
if version.repo_url:
top_element.setAttribute('url', version.repo_url)
# Add all objects in the data store base object to the XML element.
if all:
blacklist = list(self.__class__.__dict__.keys()) + list(dict.__dict__.keys())
for name in dir(self):
# Skip blacklisted objects.
if name in blacklist:
continue
# Skip special objects.
if search('^_', name):
continue
# Execute any to_xml() methods, and add that object to the blacklist.
obj = getattr(self, name)
if hasattr(obj, 'to_xml'):
obj.to_xml(xmldoc, top_element)
blacklist = blacklist + [name]
# Remove the current data pipe from the blacklist!
blacklist.remove('current_pipe')
# Add all simple python objects within the store.
fill_object_contents(xmldoc, top_element, object=self, blacklist=blacklist)
# Loop over the pipes.
for pipe in pipes:
# Create the pipe XML element and add it to the top level XML element.
pipe_element = xmldoc.createElement('pipe')
top_element.appendChild(pipe_element)
# Set the data pipe attributes.
pipe_element.setAttribute('desc', 'The contents of a relax data pipe')
pipe_element.setAttribute('name', pipe)
pipe_element.setAttribute('type', self[pipe].pipe_type)
# Fill the data pipe XML element.
self[pipe].to_xml(xmldoc, pipe_element, pipe_type=self[pipe].pipe_type)
# Write out the XML file.
file.write(xmldoc.toprettyxml(indent=' '))
def to_xml(self, doc, element, pipe_type=None):
"""Create XML elements for each spin.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param element: The element to add the spin XML elements to.
@type element: XML element object
@keyword pipe_type: The type of the pipe being converted to XML.
@type pipe_type: str
"""
# The specific analysis API object.
api = specific_analyses.api.return_api(analysis_type=pipe_type)
# Loop over the spins.
for i in range(len(self)):
# Create an XML element for this spin and add it to the higher level element.
spin_element = doc.createElement('spin')
element.appendChild(spin_element)
# Set the spin attributes.
spin_element.setAttribute('desc', 'Spin container')
spin_element.setAttribute('name', str(self[i].name))
spin_element.setAttribute('num', str(self[i].num))
# Get the spin specific object names and loop over them to get their descriptions.
object_info = []
try:
for name in api.data_names(error_names=True, sim_names=True):
# Get the description.
if hasattr(api, 'return_data_desc'):
desc = api.return_data_desc(name)
else:
desc = None
# Append the two.
object_info.append([name, desc])
except RelaxImplementError:
pass
# Add the ordered objects.
blacklist = []
for name, desc in object_info:
# Add the name to the blacklist.
blacklist.append(name)
# Skip the object if it is missing from the SpinContainer.
if not hasattr(self[i], name):
continue
# Create a new element for this object, and add it to the main element.
sub_element = doc.createElement(name)
spin_element.appendChild(sub_element)
# Add the object description.
if desc:
sub_element.setAttribute('desc', desc)
# Get the object.
object = getattr(self[i], name)
# Convert to XML.
object_to_xml(doc, sub_element, value=object)
# Add all simple python objects within the SpinContainer to the XML element.
fill_object_contents(doc, spin_element, object=self[i], blacklist=['name', 'num', 'spin'] + blacklist + list(self[i].__class__.__dict__.keys()))
