def _toXMLElement(self, parentElement):
regionElement = NeuroObject._toXMLElement(self, parentElement)
if self.ontologyTerm is not None:
ElementTree.SubElement(regionElement, 'OntologyTerm', ontologyId = str(self.ontologyTerm.ontology.identifier), ontologyTermId = str(self.ontologyTerm.identifier))
for subRegion in self.subRegions:
subRegion._toXMLElement(regionElement)
return regionElement
def _toXMLElement(self, parentElement):
neuriteElement = NeuroObject._toXMLElement(self, parentElement)
if self._pathway is not None:
neuriteElement.set("pathwayId", str(self._pathway.networkId))
for neurite in self._neurites:
neurite._toXMLElement(neuriteElement)
return neuriteElement
def _toXMLElement(self, parentElement):
neuriteElement = NeuroObject._toXMLElement(self, parentElement)
if self._pathway is not None:
neuriteElement.set('pathwayId', str(self._pathway.networkId))
for neurite in self._neurites:
neurite._toXMLElement(neuriteElement)
return neuriteElement
def _toXMLElement(self, parentElement):
synapseElement = NeuroObject._toXMLElement(self, parentElement)
ElementTree.SubElement(synapseElement, 'PreSynapticNeuriteId').text = str(self.preSynapticNeurite.networkId)
for partner in self.postSynapticPartners:
ElementTree.SubElement(synapseElement, 'PostSynapticPartnerId').text = str(partner.networkId)
if self.activation is not None:
ElementTree.SubElement(synapseElement, 'Activation').text = self.activation
return synapseElement
def _toXMLElement(self, parentElement):
arborizationElement = NeuroObject._toXMLElement(self, parentElement)
arborizationElement.set('neuriteId', str(self.neurite.networkId))
arborizationElement.set('regionId', str(self.region.networkId))
if self.sendsOutput is not None:
arborizationElement.set('sends', 'true' if self.sendsOutput else 'false')
if self.receivesInput is not None:
arborizationElement.set('receives', 'true' if self.receivesInput else 'false')
return arborizationElement
def _toXMLElement(self, parentElement):
pathwayElement = NeuroObject._toXMLElement(self, parentElement)
pathwayElement.set('region1Id', str(self.region1.networkId))
if self.region1Projects != None:
pathwayElement.set('region1Projects', str(self.region1Projects).lower())
if self.region1Projects and self.region2Activation is not None:
pathwayElement.set('region2Activation', self.region2Activation)
pathwayElement.set('region2Id', str(self.region2.networkId))
if self.region2Projects != None:
pathwayElement.set('region2Projects', str(self.region2Projects).lower())
if self.region2Projects and self.region1Activation is not None:
pathwayElement.set('region1Activation', self.region1Activation)
return pathwayElement
def _toXMLElement(self, parentElement):
#TODO need to add links and images when I get this working
neuronElement = NeuroObject._toXMLElement(self, parentElement)
if self.neuronClass is not None:
ElementTree.SubElement(neuronElement, 'Class').text = self.neuronClass.identifier
for neurotransmitter in self.neurotransmitters:
ElementTree.SubElement(neuronElement, 'Neurotransmitter').text = neurotransmitter.identifier
if self.activation is not None:
ElementTree.SubElement(neuronElement, 'Activation').text = self.activation
for function in self._functions:
ElementTree.SubElement(neuronElement, 'Function').text = function
if self.polarity is not None:
ElementTree.SubElement(neuronElement, 'Polarity').text = self.polarity
if self.region is not None:
ElementTree.SubElement(neuronElement, 'SomaRegionId').text = str(self.region.networkId)
for neurite in self._neurites:
neurite._toXMLElement(neuronElement)
return neuronElement
def _toXMLElement(self, parentElement):
#TODO need to add links and images when I get this working
neuronElement = NeuroObject._toXMLElement(self, parentElement)
if self.neuronClass is not None:
ElementTree.SubElement(neuronElement, 'Class').text = self.neuronClass.identifier
for neurotransmitter in self.neurotransmitters:
ElementTree.SubElement(neuronElement, 'Neurotransmitter').text = neurotransmitter.identifier
if self.activation is not None:
ElementTree.SubElement(neuronElement, 'Activation').text = self.activation
for function in self._functions:
ElementTree.SubElement(neuronElement, 'Function').text = function
if self.polarity is not None:
ElementTree.SubElement(neuronElement, 'Polarity').text = self.polarity
if self.region is not None:
ElementTree.SubElement(neuronElement, 'SomaRegionId').text = str(self.region.networkId)
for neurite in self._neurites:
neurite._toXMLElement(neuronElement)
return neuronElement
def _toXMLElement(self, parentElement):
gapJunctionElement = NeuroObject._toXMLElement(self, parentElement)
neurites = list(self._neurites)
gapJunctionElement.set('neurite1Id', str(neurites[0].networkId))
gapJunctionElement.set('neurite2Id', str(neurites[1].networkId))
return gapJunctionElement
def _toXMLElement(self, parentElement):
stimulusElement = NeuroObject._toXMLElement(self, parentElement)
stimulusElement.set('targetId', str(self.target.networkId))
stimulusElement.set('modality', self.modality.identifier)
return stimulusElement
def _toXMLElement(self, parentElement):
innervationElement = NeuroObject._toXMLElement(self, parentElement)
innervationElement.set('neuriteId', str(self.neurite.networkId))
innervationElement.set('muscleId', str(self.muscle.networkId))
return innervationElement
def _toXMLElement(self, parentElement):
innervationElement = NeuroObject._toXMLElement(self, parentElement)
innervationElement.set('neuriteId', str(self.neurite.networkId))
innervationElement.set('muscleId', str(self.muscle.networkId))
return innervationElement
def _toXMLElement(self, parentElement):
stimulusElement = NeuroObject._toXMLElement(self, parentElement)
stimulusElement.set('targetId', str(self.target.networkId))
stimulusElement.set('modality', self.modality.identifier)
return stimulusElement
