def buildParseGraphFromBioInfer(self, tokenElements, dependencyElements, reverseDependencies=False):
""" Returns dictionaries containing tokens and dependencies
of the graph generated from ElementTree-elements.
"""
tokensById = {}
tokensByOrigId = {}
dependenciesById = {}
prevOffset = -1000
for tokenElement in tokenElements:
node = ParseGraphNode()
node.origid = tokenElement.attrib["id"]
node.id = len(tokensById)+1
if tokenElement.attrib.has_key("POS"):
node.pos = tokenElement.attrib["POS"]
else:
node.pos = "N/A"
subtokenElement = tokenElement.find("subtoken")
node.text = subtokenElement.attrib["text"]
charFrom = int(tokenElement.attrib["charOffset"])
assert(prevOffset < charFrom)
prevOffset = charFrom
charTo = charFrom + len(subtokenElement.attrib["text"])-1
node.charOffset = (charFrom, charTo)
tokensById[node.id] = node
tokensByOrigId[node.origid] = node
#self.depByOrder = []
dependencyIndex = len(tokensById) + 99
for dependencyElement in dependencyElements:
if dependencyElement.attrib["token1"] == dependencyElement.attrib["token2"]:
continue
dependency = ParseGraphNode(True)
dependency.dependencyType = dependencyElement.attrib["type"]
if dependency.dependencyType[0] == "<":
dependency.to = tokensByOrigId[dependencyElement.attrib["token1"]]
dependency.fro = tokensByOrigId[dependencyElement.attrib["token2"]]
if reverseDependencies:
dependency.fro, dependency.to = dependency.to, dependency.fro
dependency.dependencyType = dependency.dependencyType[1:]
elif dependency.dependencyType[-1] == ">":
dependency.fro = tokensByOrigId[dependencyElement.attrib["token1"]]
dependency.to = tokensByOrigId[dependencyElement.attrib["token2"]]
if reverseDependencies:
dependency.fro, dependency.to = dependency.to, dependency.fro
dependency.dependencyType = dependency.dependencyType[:-1]
else:
sys.exit("Couldn't solve dependency type")
tokensById[dependency.fro.id].dependencies.append(dependency)
tokensById[dependency.to.id].dependencies.append(dependency)
#dependenciesById["dep_" + str(dependencyIndex) + "-mt_" + str(dependency.fro.id) + "-" + dependency.dependencyType + "-mt_" + str(dependency.to.id)] = dependency
#dependenciesById[dependencyIndex] = dependency
dependency.id = dependencyIndex # (dependency.fro.id,dependency.to.id)
assert( not dependenciesById.has_key(dependency.id) )
dependenciesById[dependency.id] = dependency
dependencyIndex += 1
return tokensById, dependenciesById
def addAnnotationDependency(self,
token1,
token2,
type,
directionality="UNIDIRECTIONAL"):
# print "TBefore:", token1, token2
token1 += 1
token2 += 1
# print "TBefore+1:", token1, token2
# POSITION 1 BEGIN
# POSITION 1 END
# print "TAfter1:", token1, token2
annotationDependency = ParseGraphNode(True)
annotationDependency.fro = self.tokensById[token1]
annotationDependency.to = self.tokensById[token2]
annotationDependency.dependencyType = type
annotationDependency.directionality = directionality
# Check for duplicates
for annDep in self.sentence.annotationDependencies:
if annDep.fro == annotationDependency.fro and \
annDep.to == annotationDependency.to and \
annDep.dependencyType == annotationDependency.dependencyType and \
annDep.directionality == annotationDependency.directionality:
return None
#self.sentence.annotationDependencies.append( (token1, token2, type) )
# print "TAfter2:", token1, token2
#self.sentence.annotationDependencies.append( (True,True,True) )
self.sentence.annotationDependencies.append(annotationDependency)
# POSITION 2 BEGIN
rv = False
for dependency in self.dependenciesById.values():
if (dependency.fro == self.tokensById[token1]
and dependency.to == self.tokensById[token2]) or (
dependency.fro == self.tokensById[token2]
and dependency.to == self.tokensById[token1]):
self.sentence.annotationDependenciesWithParseDependency += 1
rv = True
# POSITION 2 END
return rv
def buildParseGraphFromBioInfer(self,
tokenElements,
dependencyElements,
reverseDependencies=False):
""" Returns dictionaries containing tokens and dependencies
of the graph generated from ElementTree-elements.
"""
tokensById = {}
tokensByOrigId = {}
dependenciesById = {}
prevOffset = -1000
for tokenElement in tokenElements:
node = ParseGraphNode()
node.origid = tokenElement.attrib["id"]
node.id = len(tokensById) + 1
if tokenElement.attrib.has_key("POS"):
node.pos = tokenElement.attrib["POS"]
else:
node.pos = "N/A"
subtokenElement = tokenElement.find("subtoken")
node.text = subtokenElement.attrib["text"]
charFrom = int(tokenElement.attrib["charOffset"])
assert (prevOffset < charFrom)
prevOffset = charFrom
charTo = charFrom + len(subtokenElement.attrib["text"]) - 1
node.charOffset = (charFrom, charTo)
tokensById[node.id] = node
tokensByOrigId[node.origid] = node
#self.depByOrder = []
dependencyIndex = len(tokensById) + 99
for dependencyElement in dependencyElements:
if dependencyElement.attrib["token1"] == dependencyElement.attrib[
"token2"]:
continue
dependency = ParseGraphNode(True)
dependency.dependencyType = dependencyElement.attrib["type"]
if dependency.dependencyType[0] == "<":
dependency.to = tokensByOrigId[
dependencyElement.attrib["token1"]]
dependency.fro = tokensByOrigId[
dependencyElement.attrib["token2"]]
if reverseDependencies:
dependency.fro, dependency.to = dependency.to, dependency.fro
dependency.dependencyType = dependency.dependencyType[1:]
elif dependency.dependencyType[-1] == ">":
dependency.fro = tokensByOrigId[
dependencyElement.attrib["token1"]]
dependency.to = tokensByOrigId[
dependencyElement.attrib["token2"]]
if reverseDependencies:
dependency.fro, dependency.to = dependency.to, dependency.fro
dependency.dependencyType = dependency.dependencyType[:-1]
else:
sys.exit("Couldn't solve dependency type")
tokensById[dependency.fro.id].dependencies.append(dependency)
tokensById[dependency.to.id].dependencies.append(dependency)
#dependenciesById["dep_" + str(dependencyIndex) + "-mt_" + str(dependency.fro.id) + "-" + dependency.dependencyType + "-mt_" + str(dependency.to.id)] = dependency
#dependenciesById[dependencyIndex] = dependency
dependency.id = dependencyIndex # (dependency.fro.id,dependency.to.id)
assert (not dependenciesById.has_key(dependency.id))
dependenciesById[dependency.id] = dependency
dependencyIndex += 1
return tokensById, dependenciesById