Exemplo n.º 1
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 def processSubSection(self, *args, **kwargs):
     classDictionary = {'Compound':Compound, 
                        #from BioMaterial_assnlist 
                        "LabeledExtract":LabeledExtract,
                        "BioSource":BioSource, 
                        "BioSample":BioSample}
     Identifiable.iterateProcessSubSections(self, classDictionary)
Exemplo n.º 2
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 def __init__(self):
     '''
     Constructor
     '''
     Identifiable.__init__(self)
     self.chip = None
     self.probeOrder = []
Exemplo n.º 3
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 def __init__(self):
     '''
     Constructor
     '''
     Identifiable.__init__(self)
     self.chip = None
     self.probeOrder = []
Exemplo n.º 4
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 def processSubSection(self, *args, **kwargs):
     classDictionary = {
         'Compound': Compound,
         #from BioMaterial_assnlist
         "LabeledExtract": LabeledExtract,
         "BioSource": BioSource,
         "BioSample": BioSample
     }
     Identifiable.iterateProcessSubSections(self, classDictionary)
Exemplo n.º 5
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 def processSubSection(self, *args, **kwargs):
     try:
         Identifiable.processSubSection(
             self, subClass=Parameter,
             subClassKey="Parameter")  #, nodes = nodes)
     except:
         pass
     self.assessAttributes()
     self.internalGraph()
Exemplo n.º 6
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 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) 
Exemplo n.º 7
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 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()
Exemplo n.º 8
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 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
Exemplo n.º 9
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 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)
Exemplo n.º 10
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 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)
Exemplo n.º 11
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 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()
Exemplo n.º 12
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 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)
Exemplo n.º 13
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 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()
Exemplo n.º 14
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 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
Exemplo n.º 15
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 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)
Exemplo n.º 16
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 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()
Exemplo n.º 17
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 def processSubSection(self, *args,**kwargs):
     classDictionary = {"Compound_ref":Compound, 
                        "Treatment":Treatment
                        }
     Identifiable.iterateProcessSubSections(self, classDictionary)
Exemplo n.º 18
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 def __init__(self, *params):
     '''
     Constructor
     '''
     Identifiable.__init__(self)
     self.URI = None
Exemplo n.º 19
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 def internalGraph(self):
     Identifiable.noInteralGraph(self)
Exemplo n.º 20
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 def processSubSection(self, *args, **kwargs):
     Identifiable.processSubSection(self,subClass = Experiment, subClassKey = "Experiment")
Exemplo n.º 21
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 def internalGraph(self, *args, **kwargs):
     '''No instances for rdf necessary'''
     Identifiable.noInteralGraph(self)
Exemplo n.º 22
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 def processSubSection(self, *args, **kwargs):
     subClass = CompositeSequences
     subClassKey = 'CompositeSequences_assnreflist'
     nodes = self.domObject.getElementsByTagName(subClassKey)
     Identifiable.processSubSection(self, subClass, subClassKey, nodes)
Exemplo n.º 23
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 def processSubSection(self, *args, **kwargs):
     classDictionary = {"Experiment_assnlist": ExperimentList,
                        "Experiment":Experiment}
     Identifiable.processSubSection(self, subClass = ExperimentList, subClassKey = "Experiment_assnlist",
                                    classDictionary = classDictionary)
Exemplo n.º 24
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 def __init__(self):
     Identifiable.__init__(self)
Exemplo n.º 25
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 def internalGraph(self, *args, **kwargs):
     Identifiable.noInteralGraph(self)
Exemplo n.º 26
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 def internalGraph(self):
     Identifiable.noInteralGraph(self)
Exemplo n.º 27
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 def processSubSection(self, *args, **kwargs):
     classDictionary = {"Compound_ref": Compound, "Treatment": Treatment}
     Identifiable.iterateProcessSubSections(self, classDictionary)
Exemplo n.º 28
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 def internalGraph(self, *args, **kwargs):
     '''No instances for rdf necessary'''
     Identifiable.noInteralGraph(self)
Exemplo n.º 29
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 def internalGraph(self, *args, **kwargs):
     Identifiable.noInteralGraph(self)  #make no triples for package
Exemplo n.º 30
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 def internalGraph(self, *args, **kwargs):
     if self.__class__.__name__== 'BioAssay':
         Identifiable.noInteralGraph(self)
     else:
         Identifiable.internalGraph(self)
         Identifiable.addInstanceLabel(self, labelKey = 'name')
Exemplo n.º 31
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 def internalGraph(self, *args, **kwargs):
     if self.__class__.__name__ == 'BioAssay':
         Identifiable.noInteralGraph(self)
     else:
         Identifiable.internalGraph(self)
         Identifiable.addInstanceLabel(self, labelKey='name')
Exemplo n.º 32
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 def internalGraph(self, *args, **kwargs):
     Identifiable.noInteralGraph(self)
Exemplo n.º 33
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 def __init__(self):
     Identifiable.__init__(self)
     self.featureOrder = []
Exemplo n.º 34
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 def processSubSection(self, *args, **kwargs):
     try:
         Identifiable.processSubSection(self, subClass = Parameter, subClassKey = "Parameter")#, nodes = nodes)
     except: pass
     self.assessAttributes()
     self.internalGraph()
Exemplo n.º 35
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 def processSubSection(self, *args, **kwargs):
     Identifiable.processSubSection(self, Array, "Array_ref")
Exemplo n.º 36
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 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))
Exemplo n.º 37
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 def __init__(self):
     '''
     Constructor
     '''
     Identifiable.__init__(self)
Exemplo n.º 38
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 def internalGraph(self, *args, **kwargs):
     if self.__class__.__name__ == "BioMaterialPackage":
         Identifiable.noInteralGraph(self)
     else:
         Identifiable.internalGraph(self)
         Identifiable.addInstanceLabel(self, labelKey="name")
Exemplo n.º 39
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 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)
Exemplo n.º 40
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 def internalGraph(self, *args, **kwargs):
     Identifiable.noInteralGraph(self)  #make no triples for package
Exemplo n.º 41
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 def __init__(self):
     '''
     Constructor
     '''
     Identifiable.__init__(self)
     self.instanceOfClass = 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Experiment'
Exemplo n.º 42
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 def __init__(self):
     Identifiable.__init__(self)
     self.featureOrder = []
Exemplo n.º 43
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 def internalGraph(self, *args, **kwargs):
     '''reactivates internal graph, makes instance'''
     Identifiable.internalGraph(self)
Exemplo n.º 44
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 def __init__(self):
     Identifiable.__init__(self)
Exemplo n.º 45
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 def internalGraph(self, *args, **kwargs):
     if self.__class__.__name__ == "BioMaterialPackage":
         Identifiable.noInteralGraph(self)
     else:
         Identifiable.internalGraph(self)
         Identifiable.addInstanceLabel(self, labelKey="name")
Exemplo n.º 46
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 def processSubSection(self, *args, **kwargs):
     subClass = CompositeSequences
     subClassKey = 'CompositeSequences_assnreflist'
     nodes = self.domObject.getElementsByTagName(subClassKey)
     Identifiable.processSubSection(self, subClass, subClassKey, nodes)
Exemplo n.º 47
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 def internalGraph(self, *args, **kwargs):
     Identifiable.internalGraph(self)
     Identifiable.addInstanceLabel(self, labelKey="name")
Exemplo n.º 48
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 def __init__(self):
     '''
     Constructor
     '''
     Identifiable.__init__(self)