def test_RDFAnnotation_testMissingAbout(self):
withAbout = wrapString(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description rdf:about=\"#_000004\">\n" +
" <bqbiol:is>\n" + " <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:is>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" +
" </annotation>")
emptyAbout = wrapString(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description rdf:about=\"\">\n" +
" <bqbiol:is>\n" + " <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:is>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" +
" </annotation>")
noAbout = wrapString(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description>\n" + " <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:is>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" +
" </annotation>")
cvTerms = libsbml.CVTermList()
stream = libsbml.XMLInputStream(withAbout, False)
node = libsbml.XMLNode(stream)
libsbml.RDFAnnotationParser.parseRDFAnnotation(node, cvTerms)
self.assert_(cvTerms.getSize() == 1)
cvTerms = None
cvTerms = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(node, cvTerms)
self.assert_(cvTerms.getSize() == 1)
cvTerms = None
cvTerms = None
cvTerms = libsbml.CVTermList()
stream1 = libsbml.XMLInputStream(emptyAbout, False)
node1 = libsbml.XMLNode(stream1)
libsbml.RDFAnnotationParser.parseRDFAnnotation(node1, cvTerms)
self.assert_(cvTerms.getSize() == 0)
cvTerms = None
cvTerms = None
cvTerms = libsbml.CVTermList()
stream2 = libsbml.XMLInputStream(noAbout, False)
node2 = libsbml.XMLNode(stream2)
libsbml.RDFAnnotationParser.parseRDFAnnotation(node2, cvTerms)
self.assert_(cvTerms.getSize() == 0)
cvTerms = None
cvTerms = None
pass
def getModelAnnotations(self):
model = self.sbmlDocument.getModel()
annotationXML = model.getAnnotation()
lista = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML, lista)
modelAnnotations = []
for idx in range(lista.getSize()):
for idx2 in range(lista.get(idx).getResources().getLength()):
if lista.get(idx).getQualifierType():
modelAnnotations.append(
[
bioqual[lista.get(idx).getBiologicalQualifierType()],
lista.get(idx).getResources().getValue(idx2),
]
)
else:
modelAnnotations.append(
[
modqual[lista.get(idx).getModelQualifierType()],
lista.get(idx).getResources().getValue(idx2),
]
)
return modelAnnotations
def parseAnnotation(annotation):
speciesAnnotationDict = defaultdict(list)
lista = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
for idx in range(0, lista.getSize()):
for idx2 in range(0, lista.get(idx).getResources().getLength()):
resource = lista.get(idx).getResources().getValue(idx2)
qualifierType = lista.get(idx).getQualifierType()
qualifierDescription= bioqual[lista.get(idx).getBiologicalQualifierType()] if qualifierType \
else modqual[lista.get(idx).getModelQualifierType()]
speciesAnnotationDict[qualifierDescription].append(resource)
return speciesAnnotationDict
def getSpeciesAnnotationStructure(parser):
model = parser.model
for species in model.getListOfSpecies():
name = species.getName()
speciesId = species.getId()
annotation = species.getAnnotation()
lista = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
for idx in range(0, lista.getSize()):
for idx2 in range(0, lista.get(idx).getResources().getLength()):
resource = lista.get(idx).getResources().getValue(idx2)
qualifierType = lista.get(idx).getQualifierType()
qualifierDescription= bioqual[lista.get(idx).getBiologicalQualifierType()] if qualifierType \
else modqual[lista.get(idx).getModelQualifierType()]
def getAnnotationsFromFile(fileName):
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
model = document.getModel()
annotationDictionary = collections.defaultdict(list)
for species in model.getListOfSpecies():
annotationXML = species.getAnnotation()
lista = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML, lista)
if lista.getSize() == 0:
annotationDictionary[standardizeName(species.getName())] = []
for index in range(0, lista.getSize()):
#name = tmpList.getBiologicalQualifier() if tmpList.getQualifierType() == _libsbml.BIOLOGICAL_QUALIFIER else tmpList.getMo
for index2 in range(0, lista.get(index).getResources().getNumAttributes()):
annotationDictionary[standardizeName(species.getName())].append(
lista.get(index).getResources().getValue(index2))
return annotationDictionary
def getModelAnnotationFromFile(fileName):
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
model = document.getModel()
annotationXML = model.getAnnotation()
lista = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML,lista)
metaDict = []
for idx in range(lista.getSize()):
for idx2 in range(0, lista.get(idx).getResources().getLength()):
resource = lista.get(idx).getResources().getValue(idx2)
qualifierType = lista.get(idx).getQualifierType()
qualifierDescription= bioqual[lista.get(idx).getBiologicalQualifierType()] if qualifierType \
else modqual[lista.get(idx).getModelQualifierType()]
#resource = resolveAnnotation(resource)
if 'BQB' in qualifierDescription:
metaDict.append(resource)
return metaDict
def extractXMLInfo(fileName):
#if not hasattr(extractXMLInfo, 'm'):
# extractXMLInfo.m = Miriam()
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
model = document.getModel()
from collections import defaultdict
metaArray = defaultdict(list)
metaDict = {}
metaDict2 = defaultdict(list)
if model != None:
#annotation = model.getAnnotation()
#lista = libsbml.CVTermList()
#libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation,lista)
#for idx in range(0,lista.getSize()):
# resource = lista.get(idx).getResources().getValue(0)
# metaArray.add(resource)
for species in model.getListOfSpecies():
name = species.getName()
speciesId = species.getId()
annotation = species.getAnnotation()
lista = libsbml.CVTermList()
libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
for idx in range(0, lista.getSize()):
for idx2 in range(0,
lista.get(idx).getResources().getLength()):
resource = lista.get(idx).getResources().getValue(idx2)
qualifierType = lista.get(idx).getQualifierType()
qualifierDescription= bioqual[lista.get(idx).getBiologicalQualifierType()] if qualifierType \
else modqual[lista.get(idx).getModelQualifierType()]
#resource = resolveAnnotation(resource)
metaArray[qualifierDescription].append(resource)
metaDict[speciesId] = (name, resource,
qualifierDescription)
metaDict2[resource].append(
[speciesId, name, qualifierDescription])
return metaArray, metaDict, metaDict2
