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CellMLToNektar.cellml_metadata.RdfProcessor Class Reference
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Public Member Functions

def __init__
 
def __getattribute__
 
def METADATA_NAMES
 
def STIMULUS_NAMES
 
def get_rdf_from_model
 
def remove_model
 
def update_serialized_rdf
 
def create_rdf_node
 
def create_unique_id
 
def add_statement
 
def replace_statement
 
def remove_statements
 
def get_target
 
def get_targets
 
def find_variables
 
def get_all_rdf
 
def namespace_member
 

Public Attributes

 Graph
 

Private Member Functions

def _debug
 
def _load_ontology
 
def _create_new_store
 
def _add_rdf_element
 
def _serialize
 

Private Attributes

 _module
 
 _initializing
 
 _models
 
 _metadata_names
 
 _stimulus_names
 

Detailed Description

Implements CellML metadata functionality using the RDFLib library.

Definition at line 61 of file cellml_metadata.py.

Constructor & Destructor Documentation

def CellMLToNektar.cellml_metadata.RdfProcessor.__init__ (   self,
  name 
) 
Create the wrapper.

Definition at line 63 of file cellml_metadata.py.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.__getattribute__().

63 
64  def __init__(self, name):
65  """Create the wrapper."""
66  # Magic for pretending to be a module
67  self._module = sys.modules[name]
68  sys.modules[name] = self
69  self._initializing = True
70  # Map from cellml_model instances to RDF stores
71  self._models = {}
72  # Oxford metadata will be loaded lazily
73  self._metadata_names = self._stimulus_names = None
74  # Cope with differences in API between library versions
75  rdflib_major_version = int(rdflib.__version__[0])
76  if rdflib_major_version >= 3:
77  self.Graph = rdflib.Graph
78  else:
79  self.Graph = rdflib.ConjunctiveGraph
CellMLToNektar.cellml_metadata.RdfProcessor.__init__
def __init__
Definition: cellml_metadata.py:63
CellMLToNektar.cellml_metadata.RdfProcessor.Graph
Graph
Definition: cellml_metadata.py:76
CellMLToNektar.cellml_metadata.RdfProcessor._stimulus_names
_stimulus_names
Definition: cellml_metadata.py:72
CellMLToNektar.cellml_metadata.RdfProcessor._metadata_names
_metadata_names
Definition: cellml_metadata.py:72
CellMLToNektar.cellml_metadata.RdfProcessor._module
_module
Definition: cellml_metadata.py:66
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70
CellMLToNektar.cellml_metadata.RdfProcessor._initializing
_initializing
Definition: cellml_metadata.py:68

Member Function Documentation

def CellMLToNektar.cellml_metadata.RdfProcessor.__getattribute__ (   self,
  name 
) 
Provide access to real module-level variables as though they're class properties.

Definition at line 80 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor.__init__().

80 
81  def __getattribute__(self, name):
82  """Provide access to real module-level variables as though they're class properties."""
83  # call module.__init__ after import introspection is done
84  baseget = super(RdfProcessor, self).__getattribute__
85  module = baseget('_module')
86  if baseget('_initializing') and not name[:2] == '__' == name[-2:]:
87  setattr(self, '_initializing', False)
88  __init__(module)
89  try:
90  return baseget(name)
91  except AttributeError:
92  return getattr(module, name)
CellMLToNektar.cellml_metadata.RdfProcessor.__init__
def __init__
Definition: cellml_metadata.py:63
CellMLToNektar.cellml_metadata.RdfProcessor.__getattribute__
def __getattribute__
Definition: cellml_metadata.py:80
def CellMLToNektar.cellml_metadata.RdfProcessor._add_rdf_element (   self,
  cellml_model,
  rdf_text 
)
private 
Add statements to the model's graph from the given serialized RDF.

Definition at line 143 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._models, and CellMLToNektar.cellml_metadata.RdfProcessor.Graph.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

143 
144  def _add_rdf_element(self, cellml_model, rdf_text):
145  """Add statements to the model's graph from the given serialized RDF."""
146  g = self.Graph()
147  g.parse(StringIO(rdf_text))
148  rdf_model = self._models[cellml_model]
149  for stmt in g:
150  rdf_model.add(stmt)
CellMLToNektar.cellml_metadata.RdfProcessor._add_rdf_element
def _add_rdf_element
Definition: cellml_metadata.py:143
CellMLToNektar.cellml_metadata.RdfProcessor.Graph
Graph
Definition: cellml_metadata.py:76
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70
def CellMLToNektar.cellml_metadata.RdfProcessor._create_new_store (   self,
  cellml_model 
)
private 
Create a new RDF store for the given CellML model.
The new store will be available as self._models[cellml_model].

Definition at line 137 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._models, and CellMLToNektar.cellml_metadata.RdfProcessor.Graph.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

137 
138  def _create_new_store(self, cellml_model):
139  """Create a new RDF store for the given CellML model.
140  The new store will be available as self._models[cellml_model].
141  """
142  self._models[cellml_model] = self.Graph()
CellMLToNektar.cellml_metadata.RdfProcessor.Graph
Graph
Definition: cellml_metadata.py:76
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70
CellMLToNektar.cellml_metadata.RdfProcessor._create_new_store
def _create_new_store
Definition: cellml_metadata.py:137
def CellMLToNektar.cellml_metadata.RdfProcessor._debug (   args)
private

Definition at line 93 of file cellml_metadata.py.

Referenced by CellMLToNektar.optimize.PartialEvaluator._check_retargetting(), CellMLToNektar.optimize.PartialEvaluator._do_reduce_eval_loop(), CellMLToNektar.optimize.PartialEvaluator._reduce_evaluate_expression(), CellMLToNektar.optimize.PartialEvaluator._rename_var(), CellMLToNektar.cellml_metadata.RdfProcessor.add_statement(), CellMLToNektar.cellml_metadata.RdfProcessor.find_variables(), CellMLToNektar.cellml_metadata.RdfProcessor.get_target(), CellMLToNektar.cellml_metadata.RdfProcessor.namespace_member(), CellMLToNektar.cellml_metadata.RdfProcessor.remove_model(), CellMLToNektar.cellml_metadata.RdfProcessor.remove_statements(), and CellMLToNektar.cellml_metadata.RdfProcessor.replace_statement().

93 
94  def _debug(*args):
95  pycml.DEBUG('cellml-metadata', *args)
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
def CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology (   self)
private 
Load the Oxford metadata ontology the first time it's needed.

Definition at line 96 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._metadata_names, CellMLToNektar.cellml_metadata.RdfProcessor._stimulus_names, CellMLToNektar.cellml_metadata.RdfProcessor.Graph, and CellMLToNektar.cellml_metadata.RdfProcessor.namespace_member().

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.METADATA_NAMES(), and CellMLToNektar.cellml_metadata.RdfProcessor.STIMULUS_NAMES().

96 
97  def _load_ontology(self):
98  """Load the Oxford metadata ontology the first time it's needed."""
99  pycml_path = os.path.dirname(os.path.realpath(__file__))
100  oxmeta_ttl = os.path.join(pycml_path, 'oxford-metadata.ttl')
101  oxmeta_rdf = os.path.join(pycml_path, 'oxford-metadata.rdf')
102 
103  g = self.Graph()
104  # We allow a difference in modification time of 10s, so we don't get confused when checking out!
105  if os.stat(oxmeta_ttl).st_mtime > os.stat(oxmeta_rdf).st_mtime + 10.0:
106  # Try to regenerate RDF/XML version of ontology
107  try:
108  g.parse(oxmeta_ttl, format='turtle')
109  except Exception, e:
110  print >> sys.stderr, 'Unable to convert metadata from Turtle format to RDF/XML.'
111  print >> sys.stderr, 'Probably you need to upgrade rdflib to version 4.\nDetails of error:'
112  raise
113  g.serialize(oxmeta_rdf, format='xml')
114  else:
115  # Just parse the RDF/XML version
116  g.parse(oxmeta_rdf, format='xml')
117 
118  annotation_terms = list(g.subjects(rdflib.RDF.type, rdflib.URIRef(pycml.NSS['oxmeta']+u'Annotation')))
119  self._metadata_names = frozenset(map(lambda node: self.namespace_member(node, pycml.NSS['oxmeta']), annotation_terms))
120 
121  # Parameters for the stimulus current
122  self._stimulus_names = frozenset(filter(lambda name: name.startswith('membrane_stimulus_current_'), self._metadata_names))
CellMLToNektar.cellml_metadata.RdfProcessor.Graph
Graph
Definition: cellml_metadata.py:76
CellMLToNektar.cellml_metadata.RdfProcessor._stimulus_names
_stimulus_names
Definition: cellml_metadata.py:72
CellMLToNektar.cellml_metadata.RdfProcessor._metadata_names
_metadata_names
Definition: cellml_metadata.py:72
CellMLToNektar.cellml_metadata.RdfProcessor.namespace_member
def namespace_member
Definition: cellml_metadata.py:327
CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology
def _load_ontology
Definition: cellml_metadata.py:96
def CellMLToNektar.cellml_metadata.RdfProcessor._serialize (   self,
  cellml_model 
)
private 
Serialize the RDF model for this CellML model to XML.

Definition at line 151 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._models.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.update_serialized_rdf().

151 
152  def _serialize(self, cellml_model):
153  """Serialize the RDF model for this CellML model to XML."""
154  return self._models[cellml_model].serialize()
CellMLToNektar.cellml_metadata.RdfProcessor._serialize
def _serialize
Definition: cellml_metadata.py:151
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70
def CellMLToNektar.cellml_metadata.RdfProcessor.add_statement (   self,
  cellml_model,
  source,
  property,
  target 
) 
Add a statement to the model.

Definition at line 240 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug(), and CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

240 
241  def add_statement(self, cellml_model, source, property, target):
242  """Add a statement to the model."""
243  self._debug("add_statement(", source, ",", property, ",", target, ")")
244  rdf_model = self.get_rdf_from_model(cellml_model)
245  rdf_model.add((source, property, target))
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor.add_statement
def add_statement
Definition: cellml_metadata.py:240
def CellMLToNektar.cellml_metadata.RdfProcessor.create_rdf_node (   self,
  node_content = None,
  fragment_id = None 
) 
Create an RDF node.

node_content, if given, must either be a tuple (qname, namespace_uri),
or a string, in which case it is interpreted as a literal RDF node.

Alternatively, fragment_id may be given to refer to a cmeta:id within the
current model.

If neither are given, a blank node is created.

Definition at line 197 of file cellml_metadata.py.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.create_unique_id(), and CellMLToNektar.cellml_metadata.RdfProcessor.find_variables().

197 
198  def create_rdf_node(self, node_content=None, fragment_id=None):
199  """Create an RDF node.
200 
201  node_content, if given, must either be a tuple (qname, namespace_uri),
202  or a string, in which case it is interpreted as a literal RDF node.
203 
204  Alternatively, fragment_id may be given to refer to a cmeta:id within the
205  current model.
206 
207  If neither are given, a blank node is created.
208  """
209  if fragment_id:
210  node = rdflib.URIRef(str('#'+fragment_id))
211  elif node_content:
212  if type(node_content) == types.TupleType:
213  qname, nsuri = node_content
214  if nsuri[-1] not in ['#', '/']:
215  nsuri = nsuri + '#'
216  ns = rdflib.Namespace(nsuri)
217  prefix, local_name = pycml.SplitQName(qname)
218  node = ns[local_name]
219  elif type(node_content) in types.StringTypes:
220  node = rdflib.Literal(node_content)
221  else:
222  raise ValueError("Don't know how to make a node from " + str(node_content)
223  + " of type " + type(node_content))
224  else:
225  node = rdflib.BNode()
226  return node
CellMLToNektar.cellml_metadata.RdfProcessor.create_rdf_node
def create_rdf_node
Definition: cellml_metadata.py:197
def CellMLToNektar.cellml_metadata.RdfProcessor.create_unique_id (   self,
  cellml_model,
  base_id 
) 
Create a fragment identifier that hasn't already been used.

If base_id hasn't been used, it will be returned.  Otherwise, underscores will
be added until a unique id is obtained.

Definition at line 227 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor.create_rdf_node(), and CellMLToNektar.cellml_metadata.RdfProcessor.get_targets().

227 
228  def create_unique_id(self, cellml_model, base_id):
229  """Create a fragment identifier that hasn't already been used.
230 
231  If base_id hasn't been used, it will be returned. Otherwise, underscores will
232  be added until a unique id is obtained.
233  """
234  while True:
235  node = self.create_rdf_node(fragment_id=base_id)
236  if not self.get_targets(cellml_model, node, None):
237  break
238  base_id += u'_'
239  return base_id
CellMLToNektar.cellml_metadata.RdfProcessor.create_rdf_node
def create_rdf_node
Definition: cellml_metadata.py:197
CellMLToNektar.cellml_metadata.RdfProcessor.get_targets
def get_targets
Definition: cellml_metadata.py:281
CellMLToNektar.cellml_metadata.RdfProcessor.create_unique_id
def create_unique_id
Definition: cellml_metadata.py:227
def CellMLToNektar.cellml_metadata.RdfProcessor.find_variables (   self,
  cellml_model,
  property,
  value = None 
) 
Find variables in the cellml_model with the given property, and optionally value.

property (and value if given) should be a suitable input for create_rdf_node.

Will return a list of cellml_variable instances.

Definition at line 298 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug(), CellMLToNektar.cellml_metadata.RdfProcessor.create_rdf_node(), and CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

298 
299  def find_variables(self, cellml_model, property, value=None):
300  """Find variables in the cellml_model with the given property, and optionally value.
301 
302  property (and value if given) should be a suitable input for create_rdf_node.
303 
304  Will return a list of cellml_variable instances.
305  """
306  self._debug("find_variables(", property, ",", value, ")")
307  rdf_model = self.get_rdf_from_model(cellml_model)
308  property = self.create_rdf_node(property)
309  if value:
310  value = self.create_rdf_node(value)
311  vars = []
312  for result in rdf_model.subjects(property, value):
313  assert isinstance(result, rdflib.URIRef), "Non-resource annotated."
314  uri = str(result)
315  assert uri[0] == '#', "Annotation found on non-local URI"
316  var_id = uri[1:] # Strip '#'
317  var_objs = cellml_model.xml_xpath(u'*/cml:variable[@cmeta:id="%s"]' % var_id)
318  assert len(var_objs) == 1, "Didn't find a unique variable with ID " + var_id
319  vars.append(var_objs[0])
320  return vars
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.create_rdf_node
def create_rdf_node
Definition: cellml_metadata.py:197
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor.find_variables
def find_variables
Definition: cellml_metadata.py:298
def CellMLToNektar.cellml_metadata.RdfProcessor.get_all_rdf (   self,
  cellml_model 
) 
Return an iterator over all RDF triples in the model.

Definition at line 321 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

321 
322  def get_all_rdf(self, cellml_model):
323  """Return an iterator over all RDF triples in the model."""
324  rdf_model = self.get_rdf_from_model(cellml_model)
325  for triple in rdf_model:
326  yield triple
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor.get_all_rdf
def get_all_rdf
Definition: cellml_metadata.py:321
def CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model (   self,
  cellml_model 
) 
Get the RDF graph of the given CellML model.
    
If this model is already in our map, return the existing RDF store.
Otherwise, extract metadata from all RDF elements in the cellml_model,
create a new RDF graph from these, and delete the original elements.

Definition at line 155 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._add_rdf_element(), CellMLToNektar.cellml_metadata.RdfProcessor._create_new_store(), and CellMLToNektar.cellml_metadata.RdfProcessor._models.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.add_statement(), CellMLToNektar.cellml_metadata.RdfProcessor.find_variables(), CellMLToNektar.cellml_metadata.RdfProcessor.get_all_rdf(), CellMLToNektar.cellml_metadata.RdfProcessor.get_target(), CellMLToNektar.cellml_metadata.RdfProcessor.get_targets(), CellMLToNektar.cellml_metadata.RdfProcessor.remove_statements(), and CellMLToNektar.cellml_metadata.RdfProcessor.replace_statement().

155 
156  def get_rdf_from_model(self, cellml_model):
157  """Get the RDF graph of the given CellML model.
158 
159  If this model is already in our map, return the existing RDF store.
160  Otherwise, extract metadata from all RDF elements in the cellml_model,
161  create a new RDF graph from these, and delete the original elements.
162  """
163  if not cellml_model in self._models:
164  rdf_blocks = cellml_model.xml_xpath(u'//rdf:RDF')
165  self._create_new_store(cellml_model)
166  for rdf_block in rdf_blocks:
167  rdf_text = rdf_block.xml()
168  self._add_rdf_element(cellml_model, rdf_text)
169  rdf_block.xml_parent.xml_remove_child(rdf_block)
170  return self._models[cellml_model]
CellMLToNektar.cellml_metadata.RdfProcessor._add_rdf_element
def _add_rdf_element
Definition: cellml_metadata.py:143
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70
CellMLToNektar.cellml_metadata.RdfProcessor._create_new_store
def _create_new_store
Definition: cellml_metadata.py:137
def CellMLToNektar.cellml_metadata.RdfProcessor.get_target (   self,
  cellml_model,
  source,
  property 
) 
Get the target of property from source.

Returns None if no such target exists.  Throws if there is more than one match.

If the target is a literal node, returns its string value.  Otherwise returns an RDF node.

Definition at line 264 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug(), and CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

264 
265  def get_target(self, cellml_model, source, property):
266  """Get the target of property from source.
267 
268  Returns None if no such target exists. Throws if there is more than one match.
269 
270  If the target is a literal node, returns its string value. Otherwise returns an RDF node.
271  """
272  rdf_model = self.get_rdf_from_model(cellml_model)
273  try:
274  target = rdf_model.value(subject=source, predicate=property, any=False)
275  except rdflib.exceptions.UniquenessError:
276  raise ValueError("Too many targets for source " + str(source) + " and property " + str(property))
277  if isinstance(target, rdflib.Literal):
278  target = str(target)
279  self._debug("get_target(", source, ",", property, ") -> ", "'" + str(target) + "'")
280  return target
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor.get_target
def get_target
Definition: cellml_metadata.py:264
def CellMLToNektar.cellml_metadata.RdfProcessor.get_targets (   self,
  cellml_model,
  source,
  property 
) 
Get a list of all targets of property from source.

If no such targets exist, returns an empty list.
If property is None, targets of any property will be returned.
Alternatively if source is None, targets of the given property from any source will be found.

For each target, if it is a literal node then its string value is given.
Otherwise the list will contain an RDF node.

Definition at line 281 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.create_unique_id().

281 
282  def get_targets(self, cellml_model, source, property):
283  """Get a list of all targets of property from source.
284 
285  If no such targets exist, returns an empty list.
286  If property is None, targets of any property will be returned.
287  Alternatively if source is None, targets of the given property from any source will be found.
288 
289  For each target, if it is a literal node then its string value is given.
290  Otherwise the list will contain an RDF node.
291  """
292  rdf_model = self.get_rdf_from_model(cellml_model)
293  targets = list(rdf_model.objects(subject=source, predicate=property))
294  for i, target in enumerate(targets):
295  if isinstance(target, rdflib.Literal):
296  targets[i] = str(target)
297  return targets
CellMLToNektar.cellml_metadata.RdfProcessor.get_targets
def get_targets
Definition: cellml_metadata.py:281
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
def CellMLToNektar.cellml_metadata.RdfProcessor.METADATA_NAMES (   self) 
Fake a module-level constant as a property for lazy loading.

Definition at line 124 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology(), and CellMLToNektar.cellml_metadata.RdfProcessor._metadata_names.

124 
125  def METADATA_NAMES(self):
126  """Fake a module-level constant as a property for lazy loading."""
127  if self._metadata_names is None:
128  self._load_ontology()
129  return self._metadata_names
CellMLToNektar.cellml_metadata.RdfProcessor._metadata_names
_metadata_names
Definition: cellml_metadata.py:72
CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology
def _load_ontology
Definition: cellml_metadata.py:96
CellMLToNektar.cellml_metadata.RdfProcessor.METADATA_NAMES
def METADATA_NAMES
Definition: cellml_metadata.py:124
def CellMLToNektar.cellml_metadata.RdfProcessor.namespace_member (   self,
  node,
  nsuri,
  not_uri_ok = False,
  wrong_ns_ok = False 
) 
Given a URI reference RDF node and namespace URI, return the local part.

Will raise an exception if node is not a URI reference unless not_uri_ok is True.
Will raise an exception if the node doesn't live in the given namespace, unless
wrong_ns_ok is True.  In both cases, if the error is suppressed the empty string
will be returned instead.

Definition at line 327 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug().

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology().

327 
328  def namespace_member(self, node, nsuri, not_uri_ok=False, wrong_ns_ok=False):
329  """Given a URI reference RDF node and namespace URI, return the local part.
330 
331  Will raise an exception if node is not a URI reference unless not_uri_ok is True.
332  Will raise an exception if the node doesn't live in the given namespace, unless
333  wrong_ns_ok is True. In both cases, if the error is suppressed the empty string
334  will be returned instead.
335  """
336  local_part = ""
337  if not isinstance(node, rdflib.URIRef):
338  if not not_uri_ok:
339  raise ValueError("Cannot extract namespace member for a non-URI RDF node.")
340  if node.startswith(nsuri):
341  local_part = node[len(nsuri):]
342  elif not wrong_ns_ok:
343  raise ValueError("Node is not in correct namespace.")
344  self._debug("namespace_member(", node, ",", nsuri, ") = ", local_part)
345  return local_part
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.namespace_member
def namespace_member
Definition: cellml_metadata.py:327
def CellMLToNektar.cellml_metadata.RdfProcessor.remove_model (   self,
  cellml_model 
) 
The given model is being deleted / no longer needed.

Definition at line 171 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug(), and CellMLToNektar.cellml_metadata.RdfProcessor._models.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor.update_serialized_rdf().

171 
172  def remove_model(self, cellml_model):
173  """The given model is being deleted / no longer needed."""
174  if cellml_model in self._models:
175  del self._models[cellml_model]
176  self._debug('Clearing RDF state for model', cellml_model.name)
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.remove_model
def remove_model
Definition: cellml_metadata.py:171
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70
def CellMLToNektar.cellml_metadata.RdfProcessor.remove_statements (   self,
  cellml_model,
  source,
  property,
  target 
) 
Remove all statements matching (source,property,target).

Any of these may be None to match anything.

Definition at line 255 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug(), and CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

255 
256  def remove_statements(self, cellml_model, source, property, target):
257  """Remove all statements matching (source,property,target).
258 
259  Any of these may be None to match anything.
260  """
261  self._debug("remove_statements(", source, ",", property, ",", target, ")")
262  rdf_model = self.get_rdf_from_model(cellml_model)
263  rdf_model.remove((source, property, target))
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor.remove_statements
def remove_statements
Definition: cellml_metadata.py:255
def CellMLToNektar.cellml_metadata.RdfProcessor.replace_statement (   self,
  cellml_model,
  source,
  property,
  target 
) 
Add a statement to the model, avoiding duplicates.

Any existing statements with the same source and property will first be removed.

Definition at line 246 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._debug(), and CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model().

246 
247  def replace_statement(self, cellml_model, source, property, target):
248  """Add a statement to the model, avoiding duplicates.
249 
250  Any existing statements with the same source and property will first be removed.
251  """
252  self._debug("replace_statement(", source, ",", property, ",", target, ")")
253  rdf_model = self.get_rdf_from_model(cellml_model)
254  rdf_model.set((source, property, target))
CellMLToNektar.cellml_metadata.RdfProcessor._debug
def _debug
Definition: cellml_metadata.py:93
CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model
def get_rdf_from_model
Definition: cellml_metadata.py:155
CellMLToNektar.cellml_metadata.RdfProcessor.replace_statement
def replace_statement
Definition: cellml_metadata.py:246
def CellMLToNektar.cellml_metadata.RdfProcessor.STIMULUS_NAMES (   self) 
Fake a module-level constant as a property for lazy loading.

Definition at line 131 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology(), and CellMLToNektar.cellml_metadata.RdfProcessor._stimulus_names.

131 
132  def STIMULUS_NAMES(self):
133  """Fake a module-level constant as a property for lazy loading."""
134  if self._stimulus_names is None:
135  self._load_ontology()
136  return self._stimulus_names
CellMLToNektar.cellml_metadata.RdfProcessor._stimulus_names
_stimulus_names
Definition: cellml_metadata.py:72
CellMLToNektar.cellml_metadata.RdfProcessor.STIMULUS_NAMES
def STIMULUS_NAMES
Definition: cellml_metadata.py:131
CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology
def _load_ontology
Definition: cellml_metadata.py:96
def CellMLToNektar.cellml_metadata.RdfProcessor.update_serialized_rdf (   self,
  cellml_model 
) 
Ensure the RDF serialized into the given CellML model is up-to-date.

If we have done any metadata processing on the given model, will serialize
our RDF store into the rdf:RDF element child of the model.

Definition at line 177 of file cellml_metadata.py.

References CellMLToNektar.cellml_metadata.RdfProcessor._models, CellMLToNektar.cellml_metadata.RdfProcessor._serialize(), and CellMLToNektar.cellml_metadata.RdfProcessor.remove_model().

177 
178  def update_serialized_rdf(self, cellml_model):
179  """Ensure the RDF serialized into the given CellML model is up-to-date.
180 
181  If we have done any metadata processing on the given model, will serialize
182  our RDF store into the rdf:RDF element child of the model.
183  """
184  if cellml_model in self._models:
185  # Paranoia: ensure it doesn't already contain serialized RDF
186  rdf_blocks = cellml_model.xml_xpath(u'//rdf:RDF')
187  if rdf_blocks:
188  pycml.LOG('cellml-metadata', logging.WARNING, 'Removing existing RDF in model.')
189  for rdf_block in rdf_blocks:
190  rdf_block.xml_parent.xml_remove_child(rdf_block)
191  # Serialize the RDF model into cellml_model.RDF
192  rdf_text = self._serialize(cellml_model)
193  rdf_doc = pycml.amara.parse(rdf_text)
194  cellml_model.xml_append(rdf_doc.RDF)
195  # Remove the RDF model
196  self.remove_model(cellml_model)
CellMLToNektar.cellml_metadata.RdfProcessor.update_serialized_rdf
def update_serialized_rdf
Definition: cellml_metadata.py:177
CellMLToNektar.cellml_metadata.RdfProcessor._serialize
def _serialize
Definition: cellml_metadata.py:151
CellMLToNektar.cellml_metadata.RdfProcessor.remove_model
def remove_model
Definition: cellml_metadata.py:171
CellMLToNektar.cellml_metadata.RdfProcessor._models
_models
Definition: cellml_metadata.py:70

Member Data Documentation

CellMLToNektar.cellml_metadata.RdfProcessor._initializing
private

Definition at line 68 of file cellml_metadata.py.

CellMLToNektar.cellml_metadata.RdfProcessor._metadata_names
private

Definition at line 72 of file cellml_metadata.py.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology(), and CellMLToNektar.cellml_metadata.RdfProcessor.METADATA_NAMES().

CellMLToNektar.cellml_metadata.RdfProcessor._models
private

Definition at line 70 of file cellml_metadata.py.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor._add_rdf_element(), CellMLToNektar.cellml_metadata.RdfProcessor._create_new_store(), CellMLToNektar.cellml_metadata.RdfProcessor._serialize(), CellMLToNektar.cellml_metadata.RdfProcessor.get_rdf_from_model(), CellMLToNektar.cellml_metadata.RdfProcessor.remove_model(), and CellMLToNektar.cellml_metadata.RdfProcessor.update_serialized_rdf().

CellMLToNektar.cellml_metadata.RdfProcessor._module
private

Definition at line 66 of file cellml_metadata.py.

CellMLToNektar.cellml_metadata.RdfProcessor._stimulus_names
private

Definition at line 72 of file cellml_metadata.py.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology(), and CellMLToNektar.cellml_metadata.RdfProcessor.STIMULUS_NAMES().

CellMLToNektar.cellml_metadata.RdfProcessor.Graph

Definition at line 76 of file cellml_metadata.py.

Referenced by CellMLToNektar.cellml_metadata.RdfProcessor._add_rdf_element(), CellMLToNektar.cellml_metadata.RdfProcessor._create_new_store(), and CellMLToNektar.cellml_metadata.RdfProcessor._load_ontology().

Generated on Wed Mar 8 2017 12:29:21 for Nektar++ by   doxygen 1.8.8