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 __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 internalGraph(self):
Identifiable.noInteralGraph(self)
def processSubSection(self, *args, **kwargs):
classDictionary = {"Compound_ref": Compound, "Treatment": Treatment}
Identifiable.iterateProcessSubSections(self, classDictionary)
def internalGraph(self, *args, **kwargs):
'''No instances for rdf necessary'''
Identifiable.noInteralGraph(self)
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 internalGraph(self, *args, **kwargs):
Identifiable.noInteralGraph(self)
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 internalGraph(self, *args, **kwargs):
Identifiable.noInteralGraph(self) #make no triples for package
def __init__(self):
'''
Constructor
'''
Identifiable.__init__(self)
self.instanceOfClass = 'http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Experiment'
def __init__(self):
Identifiable.__init__(self)
self.featureOrder = []
def internalGraph(self, *args, **kwargs):
'''reactivates internal graph, makes instance'''
Identifiable.internalGraph(self)
def __init__(self):
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 processSubSection(self, *args, **kwargs):
subClass = CompositeSequences
subClassKey = 'CompositeSequences_assnreflist'
nodes = self.domObject.getElementsByTagName(subClassKey)
Identifiable.processSubSection(self, subClass, subClassKey, nodes)
def internalGraph(self, *args, **kwargs):
Identifiable.internalGraph(self)
Identifiable.addInstanceLabel(self, labelKey="name")
def __init__(self):
'''
Constructor
'''
Identifiable.__init__(self)
