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 __init__(self, abstract, useTrialReports=True):
""" build list of locations """
self.abstract = abstract
self.source = ''
self.locationTemplates = []
self.locationStrings = []
if useTrialReports and self.abstract.report != None \
and len(self.abstract.report.locations) > 0:
for country in self.abstract.report.locations:
self.locationStrings.append(country)
self.source = 'trial_registry'
else:
self.locationTemplates = createMergedList(abstract, 'location')
self.source = 'abstract'
if len(self.locationTemplates) == 0 \
and len(self.abstract.affiliationSentences) > 0:
# use location in the affiliation section of the abstract
self.source = 'affiliation'
s = self.abstract.affiliationSentences[0]
lastTokenIndex = len(s.tokens) - 1
if s.tokens[lastTokenIndex].text == '.':
lastTokenIndex -= 1
if lastTokenIndex > 0 and s.tokens[lastTokenIndex].isLocation(
):
country = s.tokens[lastTokenIndex].text
i = lastTokenIndex - 1
while i >= 0 and s.tokens[i].text != ',':
country = s.tokens[i].text + ' ' + country
i -= 1
self.locationStrings.append(country)
def __init__(self, abstract, useTrialReports=True):
""" build list of locations """
self.abstract = abstract
self.source = ''
self.locationTemplates = []
self.locationStrings = []
if useTrialReports and self.abstract.report != None \
and len(self.abstract.report.locations) > 0:
for country in self.abstract.report.locations:
self.locationStrings.append(country)
self.source = 'trial_registry'
else:
self.locationTemplates = createMergedList(abstract, 'location')
self.source = 'abstract'
if len(self.locationTemplates) == 0 \
and len(self.abstract.affiliationSentences) > 0:
# use location in the affiliation section of the abstract
self.source = 'affiliation'
s = self.abstract.affiliationSentences[0]
lastTokenIndex = len(s.tokens)-1
if s.tokens[lastTokenIndex].text == '.':
lastTokenIndex -= 1
if lastTokenIndex > 0 and s.tokens[lastTokenIndex].isLocation():
country = s.tokens[lastTokenIndex].text
i = lastTokenIndex - 1
while i >= 0 and s.tokens[i].text != ',':
country = s.tokens[i].text + ' ' + country
i -= 1
self.locationStrings.append(country)