def processSubSection(self, *args, **kwargs): classDictionary = {'Compound':Compound, #from BioMaterial_assnlist "LabeledExtract":LabeledExtract, "BioSource":BioSource, "BioSample":BioSample} Identifiable.iterateProcessSubSections(self, classDictionary)
def __init__(self): ''' Constructor ''' Identifiable.__init__(self) self.chip = None self.probeOrder = []
def processSubSection(self, *args, **kwargs): classDictionary = { 'Compound': Compound, #from BioMaterial_assnlist "LabeledExtract": LabeledExtract, "BioSource": BioSource, "BioSample": BioSample } Identifiable.iterateProcessSubSections(self, classDictionary)
def processSubSection(self, *args, **kwargs): try: Identifiable.processSubSection( self, subClass=Parameter, subClassKey="Parameter") #, nodes = nodes) except: pass self.assessAttributes() self.internalGraph()
def processSubSection(self, *args, **kwargs): classDictionary = {"MeasuredBioAssayData":MeasuredBioAssayData, "DerivedBioAssayData":DerivedBioAssayData, #from Experiment section: "MeasuredBioAssayData_ref": MeasuredBioAssayData, "DerivedBioAssayData_ref": DerivedBioAssayData} for subClassKey, subClass in classDictionary.iteritems(): if self.subsections.get(subClassKey) == None: self.subsections[subClassKey] = [] Identifiable.processSubSection(self, subClass, subClassKey)
def processSubSection(self, *args, **kwargs): '''Terminal process. ''' subNodes = self.domObject.getElementsByTagName("Organization_ref") try: Identifiable.processSubSection(self,Organization, "Organization_ref", subNodes) except: print "failed in Person Internally" try: self.assessAttributes() except: pass self.internalGraph()
def processSubSection(self, subClass = None, subClassKey =None,nodes = None, classDictionary = None, *args, **kwargs): '''function to call to process AuditAndSecurity's subsections ''' classDictionary = {"Contact_assnlist":Contact}#, "Organization":Organization, for subClassKey, subClass in classDictionary.iteritems(): try: Identifiable.processSubSection(self, subClass = subClass, subClassKey = subClassKey, nodes = nodes, classDictionary = classDictionary) except: print "did not get through subsection %s within AuditAndSecurity"%subClassKey
def processSubSection(self, *args, **kwargs): classDictionary = { "MeasuredBioAssayData": MeasuredBioAssayData, "DerivedBioAssayData": DerivedBioAssayData, #from Experiment section: "MeasuredBioAssayData_ref": MeasuredBioAssayData, "DerivedBioAssayData_ref": DerivedBioAssayData } for subClassKey, subClass in classDictionary.iteritems(): if self.subsections.get(subClassKey) == None: self.subsections[subClassKey] = [] Identifiable.processSubSection(self, subClass, subClassKey)
def processSubSection(self, subClass = None, subClassKey = None, nodes = None, classDictionary = None, *args, **kwargs): if subClass != None: Identifiable.processSubSection(self, subClass, subClassKey, nodes, classDictionary) if classDictionary == None: classDictionary = {'QuantitationTypeDimension_ref':QuantitationTypeDimension, 'CompositeSequenceDimension_ref':CompositeSequenceDimension, #DesignElementDimensionList? "BioDataValues_assn":BioDataValues, # may need to go straight to BioDataCube "Transformation":Transformation, "DesignElementDimension_assnref":DesignElementDimensionList, } self.iterateProcessSubSections(classDictionary)
def processSubSection(self, *args, **kwargs): '''Terminal process. ''' subNodes = self.domObject.getElementsByTagName("Organization_ref") try: Identifiable.processSubSection(self, Organization, "Organization_ref", subNodes) except: print "failed in Person Internally" try: self.assessAttributes() except: pass self.internalGraph()
def processSubSection(self, *args, **kwargs): classDictionary = {"BioAssayData_assnreflist":BioAssayData, "Person_ref": Person, "Organization_ref":Organization, #"Description": Description, "BioAssays_assnreflist":BioAssay } try: self.assessAttributes() except: pass for subClassKey, subClass in classDictionary.iteritems(): if self.subsections.get(subClassKey) == None: self.subsections[subClassKey] = [] Identifiable.processSubSection(self, subClass, subClassKey)
def processSubSection(self, subClass = None, subClassKey = None, nodes = None, classDictionary = None, *args, **kwargs): ''' Imports Person/Organization to avoid conflicts. ''' from Person import Person from Organization import Organization classDictionary = {'Person':Person, "Organization":Organization} for subClassKey, subClass in classDictionary.iteritems(): try: Identifiable.processSubSection(self, subClass = subClass, subClassKey = subClassKey, nodes = None, classDictionary = classDictionary) except: pass self.internalGraph()
def processSubSection(self, subClass=None, subClassKey=None, nodes=None, classDictionary=None, *args, **kwargs): '''function to call to process AuditAndSecurity's subsections ''' classDictionary = { "Contact_assnlist": Contact } #, "Organization":Organization, for subClassKey, subClass in classDictionary.iteritems(): try: Identifiable.processSubSection(self, subClass=subClass, subClassKey=subClassKey, nodes=nodes, classDictionary=classDictionary) except: print "did not get through subsection %s within AuditAndSecurity" % subClassKey
def processSubSection(self, subClass=None, subClassKey=None, nodes=None, classDictionary=None, *args, **kwargs): if subClass != None: Identifiable.processSubSection(self, subClass, subClassKey, nodes, classDictionary) if classDictionary == None: classDictionary = { 'QuantitationTypeDimension_ref': QuantitationTypeDimension, 'CompositeSequenceDimension_ref': CompositeSequenceDimension, #DesignElementDimensionList? "BioDataValues_assn": BioDataValues, # may need to go straight to BioDataCube "Transformation": Transformation, "DesignElementDimension_assnref": DesignElementDimensionList, } self.iterateProcessSubSections(classDictionary)
def processSubSection(self, subClass=None, subClassKey=None, nodes=None, classDictionary=None, *args, **kwargs): ''' Imports Person/Organization to avoid conflicts. ''' from Person import Person from Organization import Organization classDictionary = {'Person': Person, "Organization": Organization} for subClassKey, subClass in classDictionary.iteritems(): try: Identifiable.processSubSection(self, subClass=subClass, subClassKey=subClassKey, nodes=None, classDictionary=classDictionary) except: pass self.internalGraph()
def processSubSection(self, *args,**kwargs): classDictionary = {"Compound_ref":Compound, "Treatment":Treatment } Identifiable.iterateProcessSubSections(self, classDictionary)
def __init__(self, *params): ''' Constructor ''' Identifiable.__init__(self) self.URI = None
def internalGraph(self): Identifiable.noInteralGraph(self)
def processSubSection(self, *args, **kwargs): Identifiable.processSubSection(self,subClass = Experiment, subClassKey = "Experiment")
def internalGraph(self, *args, **kwargs): '''No instances for rdf necessary''' Identifiable.noInteralGraph(self)
def processSubSection(self, *args, **kwargs): subClass = CompositeSequences subClassKey = 'CompositeSequences_assnreflist' nodes = self.domObject.getElementsByTagName(subClassKey) Identifiable.processSubSection(self, subClass, subClassKey, nodes)
def processSubSection(self, *args, **kwargs): classDictionary = {"Experiment_assnlist": ExperimentList, "Experiment":Experiment} Identifiable.processSubSection(self, subClass = ExperimentList, subClassKey = "Experiment_assnlist", classDictionary = classDictionary)
def __init__(self): Identifiable.__init__(self)
def internalGraph(self, *args, **kwargs): Identifiable.noInteralGraph(self)
def processSubSection(self, *args, **kwargs): classDictionary = {"Compound_ref": Compound, "Treatment": Treatment} Identifiable.iterateProcessSubSections(self, classDictionary)
def internalGraph(self, *args, **kwargs): Identifiable.noInteralGraph(self) #make no triples for package
def internalGraph(self, *args, **kwargs): if self.__class__.__name__== 'BioAssay': Identifiable.noInteralGraph(self) else: Identifiable.internalGraph(self) Identifiable.addInstanceLabel(self, labelKey = 'name')
def internalGraph(self, *args, **kwargs): if self.__class__.__name__ == 'BioAssay': Identifiable.noInteralGraph(self) else: Identifiable.internalGraph(self) Identifiable.addInstanceLabel(self, labelKey='name')
def __init__(self): Identifiable.__init__(self) self.featureOrder = []
def processSubSection(self, *args, **kwargs): try: Identifiable.processSubSection(self, subClass = Parameter, subClassKey = "Parameter")#, nodes = nodes) except: pass self.assessAttributes() self.internalGraph()
def processSubSection(self, *args, **kwargs): Identifiable.processSubSection(self, Array, "Array_ref")
def add_node(self, node: Identifiable): self.nodes.append(node) node.index = len(self.nodes) - 1 for row in self.adj_mat: row.append(0) self.adj_mat.append([0] * (len(self.adj_mat) + 1))
def __init__(self): ''' Constructor ''' Identifiable.__init__(self)
def internalGraph(self, *args, **kwargs): if self.__class__.__name__ == "BioMaterialPackage": Identifiable.noInteralGraph(self) else: Identifiable.internalGraph(self) Identifiable.addInstanceLabel(self, labelKey="name")
def internalGraph(self, *args, **kwargs): '''Empty method prevents instances from being created. Instances of items within will be created if 'internalGraph' method is enabled with subClasses. ''' Identifiable.noInteralGraph(self)
def __init__(self): ''' Constructor ''' Identifiable.__init__(self) self.instanceOfClass = 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Experiment'
def internalGraph(self, *args, **kwargs): '''reactivates internal graph, makes instance''' Identifiable.internalGraph(self)
def internalGraph(self, *args, **kwargs): Identifiable.internalGraph(self) Identifiable.addInstanceLabel(self, labelKey="name")