def __init__(self, abstract, useAnnotated=False, useTrialReports=True):
""" create a list of groups and common medical conditions given
an abstact object. """
self.abstract = abstract
self.useTrialReports = useTrialReports
self.nTrueGroups = 0
self.nTrueConditions = 0
self.nTrueGroupSizes = 0
if useAnnotated == True:
self.groupTemplates = abstract.annotatedEntities.getList('group')
self.ageTemplates = createAnnotatedMergedList(abstract, 'age')
self.conditionTemplates = abstract.annotatedEntities.getList('condition')
populationTemplates = createAnnotatedMergedList(abstract, 'population')
else:
self.groupTemplates = abstract.entities.getList('group')
self.ageTemplates = createMergedList(abstract, 'age')
self.conditionTemplates = abstract.entities.getList('condition')
populationTemplates = createMergedList(abstract, 'population')
self.ageInfo = AgeInfo(self.ageTemplates, abstract, self.useTrialReports)
self.gender = Gender(populationTemplates, abstract, self.useTrialReports)
# filter useless population terms
self.populationTemplates = []
for pTemplate in populationTemplates:
if pTemplate.isInteresting() > 0:
# term is informative, keep it
self.populationTemplates.append(pTemplate)
class SubjectList:
""" Maintain list of treatment groups and common medical conditions
for a given abstract. """
groupTemplates = None # list of group templates for the abstract
ageInfo = None # information describing age ranges of subjects
ageTemplates = None
conditionTemplates = None # list of templates describing common conditions
populationTemplates = None
abstract = None
gender = None
useTrialReports = None
nTrueGroups = 0
nTrueConditions = 0
nTrueGroupSizes = 0
def __init__(self, abstract, useAnnotated=False, useTrialReports=True):
""" create a list of groups and common medical conditions given
an abstact object. """
self.abstract = abstract
self.useTrialReports = useTrialReports
self.nTrueGroups = 0
self.nTrueConditions = 0
self.nTrueGroupSizes = 0
if useAnnotated == True:
self.groupTemplates = abstract.annotatedEntities.getList('group')
self.ageTemplates = createAnnotatedMergedList(abstract, 'age')
self.conditionTemplates = abstract.annotatedEntities.getList('condition')
populationTemplates = createAnnotatedMergedList(abstract, 'population')
else:
self.groupTemplates = abstract.entities.getList('group')
self.ageTemplates = createMergedList(abstract, 'age')
self.conditionTemplates = abstract.entities.getList('condition')
populationTemplates = createMergedList(abstract, 'population')
self.ageInfo = AgeInfo(self.ageTemplates, abstract, self.useTrialReports)
self.gender = Gender(populationTemplates, abstract, self.useTrialReports)
# filter useless population terms
self.populationTemplates = []
for pTemplate in populationTemplates:
if pTemplate.isInteresting() > 0:
# term is informative, keep it
self.populationTemplates.append(pTemplate)
def computeStatistics(self, errorOut):
""" Count RPF statistics for each unique AGE, CONDITION, POPULATION entity
statOut = file stream for RPF stats for all parts of summarization system
errorOut = file stream for TPs, FPs, FNs
return hash of IRstats, one for each mention type, keyed by mention type
"""
stats = {}
self.nTrueGroupSizes = 0
aAgeTemplates = createAnnotatedMergedList(self.abstract, 'age')
errorOut.write('age:\n')
stats['age'] = self.ageInfo.countAgeMatches(aAgeTemplates, errorOut)
errorOut.write('condition:\n')
aConditionTemplates = self.abstract.annotatedEntities.getList('condition')
stats['condition'] = countMatches(aConditionTemplates, \
self.conditionTemplates, errorOut)
errorOut.write('group:\n')
aGroupTemplates = self.abstract.annotatedEntities.getList('group')
stats['group'] = countMatches(aGroupTemplates, self.groupTemplates, errorOut)
self.nTrueConditions = len(aConditionTemplates)
self.nTrueGroups = len(aGroupTemplates)
errorOut.write('group size:\n')
gsStats = IRstats()
gsFound = set([])
for gTemplate in self.groupTemplates:
gSize = gTemplate.getSize(maxSize=True)
if gSize != 0:
# look for group size match in sizes for annotated group
found = False
if gTemplate.matchedTemplate != None:
for trueGSize in gTemplate.matchedTemplate.sizes:
if gSize == trueGSize.value:
found = True
break
if found:
# group size is correct
gsStats.incTP()
errorOut.write(' +TP: %s size = %d\n' % (gTemplate.name, gSize))
gTemplate.groupSizeEvaluation.markCorrect()
gsFound.add(gTemplate.matchedTemplate)
else:
# group size is incorrect
gsStats.incFP()
errorOut.write(' -FP: %s size = %d\n' % (gTemplate.name, gSize))
gTemplate.groupSizeEvaluation.markIncorrect()
# look for false negatives
for trueTemplate in aGroupTemplates:
if trueTemplate not in gsFound and trueTemplate.matchedTemplate != None and trueTemplate.getSize() > 0:
# there should be a group size for this group
gsStats.incFN()
errorOut.write(' -FN: %s size = %d\n' % \
(trueTemplate.name, trueTemplate.getSize()))
stats['group size'] = gsStats
self.nTrueGroupSizes = gsStats.tp + gsStats.fn
# errorOut.write('population:\n')
# templates = createAnnotatedMergedList(self.abstract, 'population')
# aPopulationTemplates = []
# for pTemplate in templates:
# if pTemplate.isInteresting() > 0:
# # term is informative, keep it
# aPopulationTemplates.append(pTemplate)
# stats['population'] = self.countMatches(aPopulationTemplates, \
# self.populationTemplates, errorOut)
return stats
def getXML(self, doc, idPrefix):
""" return an xml node that contains information about subjects
in the study. """
# if len(self.groupTemplates) == 0 and len(self.populationTemplates) == 0 \
# and len(self.ageTemplates) == 0 and len(self.conditionTemplates) == 0:
# return None
subjectListNode = doc.createElement('Subjects')
eligibilityNode = doc.createElement('Eligibility')
subjectListNode.appendChild(eligibilityNode)
# for pTemplate in self.populationTemplates:
# popNode = doc.createElement('Population')
# # setUMLSAttribute(popNode, pTemplate)
# nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', pTemplate.name)
# popNode.appendChild(nameNode)
# eligibilityNode.appendChild(popNode)
eligibilityNode.appendChild(self.gender.getXML(doc, idPrefix))
if len(self.ageInfo.ageValues) > 0:
eligibilityNode.appendChild(self.ageInfo.getXML(doc, idPrefix))
for cTemplate in self.conditionTemplates:
cNode = doc.createElement('Criteria')
cNode.setAttribute('source', 'abstract')
id = idPrefix+cTemplate.id
cTemplate.evaluation.id = id
cNode.setAttribute('Id', id)
# setUMLSAttribute(cNode, cTemplate)
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', cTemplate.name)
cNode.appendChild(nameNode)
type = 'unknown'
firstToken = cTemplate.mention.tokens[0]
if firstToken.text == 'with' or firstToken.lemma == 'have':
type = 'inclusion'
elif firstToken.text == 'without':
type = 'exclusion'
cNode.setAttribute('type', type)
eligibilityNode.appendChild(cNode)
if self.useTrialReports and self.abstract.report != None:
icCount = 0
ecCount = 0
for criteria in self.abstract.report.inclusionCriteria:
cNode = doc.createElement('Criteria')
cNode.setAttribute('source', 'trial_registry')
cNode.setAttribute('Id', idPrefix+'ic'+str(icCount))
icCount += 1
text = criteria.sentences[0].toString()
for i in range(1, len(criteria.sentences)):
text = text + ' ' + criteria.sentences[i].toString()
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', text)
cNode.appendChild(nameNode)
cNode.setAttribute('type', 'inclusion')
eligibilityNode.appendChild(cNode)
for criteria in self.abstract.report.exclusionCriteria:
cNode = doc.createElement('Criteria')
cNode.setAttribute('source', 'trial_registry')
cNode.setAttribute('Id', idPrefix+'ec'+str(ecCount))
ecCount += 1
text = criteria.sentences[0].toString()
for i in range(1, len(criteria.sentences)):
text = text + ' ' + criteria.sentences[i].toString()
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', text)
cNode.appendChild(nameNode)
cNode.setAttribute('type', 'exclusion')
eligibilityNode.appendChild(cNode)
for gTemplate in self.groupTemplates:
groupNode = doc.createElement('Group')
id = idPrefix+gTemplate.id
gTemplate.evaluation.id = idPrefix+gTemplate.id
groupNode.setAttribute('Id', id)
groupNode.setAttribute('Role', gTemplate.role)
gSize = gTemplate.getSize(maxSize=True)
if gSize > 0:
sNode = xmlutil.createNodeWithTextChild(doc, 'Size', str(gSize))
id = idPrefix+gTemplate.id+'size'
gTemplate.groupSizeEvaluation.id = id
sNode.setAttribute('Id', id)
groupNode.appendChild(sNode)
# setUMLSAttribute(groupNode, gTemplate)
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', gTemplate.name)
groupNode.appendChild(nameNode)
subjectListNode.appendChild(groupNode)
return subjectListNode
def writeHTML(self, out):
""" write subject list information to given output stream in html format. """
out.write('<h3>Subjects</h3>\n')
# out.write('<b>Population:</b><ul>\n')
# for template in self.populationTemplates:
# out.write('<li>'+template.name+'</li>')
# out.write('</ul><b>Gender:</b><ul>\n')
# out.write('<li>'+self.gender.value)
# if self.gender.source != None:
# out.write(' ('+self.gender.source+')')
# out.write('</li></ul>\n')
out.write('</ul><b>Age:</b><ul>\n')
for type,av in self.ageInfo.ageValues.items():
out.write('<li>'+av.type+': '+str(av.value)+' ')
if av.units != None:
out.write(av.units)
# out.write(' ('+av.source+')</li>\n')
out.write(' </li>\n')
out.write('</ul>')
out.write('</ul><b>Condition:</b><ul>\n')
for template in self.conditionTemplates:
out.write('<li>'+template.name+'</li>')
out.write('</ul><b>Groups:</b><ul>\n')
for template in self.groupTemplates:
size = 'unknown'
gSize = template.getSize(maxSize=True)
if gSize > 0:
size = str(gSize)
out.write('<li>'+template.name+' (size=' + size + ')</li>')
# out.write('<li>'+template.name+' (id='+template.id+', role=' \
# +template.role+', size=' + size + ')</li>')
out.write('</ul>\n')
def writeEvaluationForm(self, out):
out.write('GENDER:\n\n')
writeEvaluationElement(self.gender.value, out)
out.write('AGE:\n\n')
for type,av in self.ageInfo.ageValues.items():
avString = av.type+': '+str(av.value)
if av.units != None:
avString += ' '+av.units
writeEvaluationElement(avString, out)
writeElementsMissing('ages', out)
out.write('CONDITIONS:\n\n')
for template in self.conditionTemplates:
writeEvaluationElement(template.name, out)
writeElementsMissing('conditions', out)
out.write('GROUPS:\n\n')
for template in self.groupTemplates:
writeEvaluationElement(template.name, out)
gSize = template.getSize(maxSize=True)
if gSize > 0:
writeEvaluationElement('size: %d' % gSize, out, indentLevel=1)
writeElementsMissing('groups', out)