def pycontextnlp_markup_sentence(s, modifiers, targets, prune_inactive=True):
markup = pyConText.ConTextMarkup()
markup.setRawText(s)
markup.cleanText()
markup.markItems(modifiers, mode="modifier")
markup.markItems(targets, mode="target")
markup.pruneMarks()
markup.dropMarks('Exclusion')
markup.applyModifiers()
markup.pruneSelfModifyingRelationships()
if prune_inactive:
markup.dropInactiveModifiers()
list_negated_edges = []
for edge in markup.edges():
# modifier_category = edge[0].getCategory()
# if('neg' in modifier_category[0]):
# # print(edge)
# list_negated_edges.append(edge)
list_negated_edges.append(edge)
return list_negated_edges
def markup_sentence(s, modifiers, targets, prune_inactive=True):
"""
"""
markup = pyConText.ConTextMarkup()
markup.setRawText(s)
markup.cleanText()
markup.markItems(my_modifiers, mode="modifier")
markup.markItems(my_targets, mode="target")
markup.pruneMarks()
markup.dropMarks('Exclusion')
# apply modifiers to any targets within the modifiers scope
markup.applyModifiers()
markup.pruneSelfModifyingRelationships()
if prune_inactive:
markup.dropInactiveModifiers()
return markup
def test_1(self):
sent1 = 'IMPRESSION: 1. R/O STUDY DEMONSTRATING NO GROSS EVIDENCE OF SIGNIFICANT PULMONARY EMBOLISM.'
print(os.getcwd())
modifiers = itemData.get_items(
os.path.join(os.getcwd(), "../../KB/pneumonia_modifiers.yml"))
targets = itemData.get_items(
os.path.join(os.getcwd(), "../../KB/pneumonia_targets.yml"))
markup = pyConText.ConTextMarkup()
markup.setRawText(sent1.lower())
markup.markItems(modifiers, mode="modifier")
markup.markItems(targets, mode="target")
found = False
for node in markup.nodes(data=True):
if 'r/o' in str(node):
found = True
assert found
def analyze_sentence(sentence, modifiers, targets, tagExperiencer=False):
context = pyConText.ConTextDocument()
markup = pyConText.ConTextMarkup()
markup.setRawText(sentence)
markup.markItems(modifiers, mode="modifier")
markup.markItems(targets, mode="target")
markup.pruneMarks()
markup.dropMarks('Exclusion')
markup.applyModifiers()
markup.dropInactiveModifiers()
markup.updateScopes()
context.addMarkup(markup)
g = context.getDocumentGraph()
ma = g.getMarkedTargets()
tst = []
details = []
found = {}
for te in ma:
#print ma
tmp1, tmp2 = getNegationValue(g, te)
if tagExperiencer:
e1, e2 = getExperiencerValue(g, te)
if e1 != 'Other':
tst.append(tmp1)
details.append(tmp2)
found[tmp2] = Counter(tmp1)
else:
tst.append(tmp1)
details.append(tmp2)
found[tmp2] = Counter(tmp1)
return tst, details
"https://raw.githubusercontent.com/chapmanbe/pyConTextNLP/20c752d6bd5191833f21ab81fc7f41877dca1db6/KB/pneumonia_modifiers.yml"
)
for i in range(len(sentences)):
# omg
targets = []
with open('./hpo_labels.txt') as labelfile:
reader = csv.reader(labelfile, delimiter='\t')
for row in reader:
if (row[1] == iris[i]):
targets.append(contextItem((row[0], row[1], '', '')))
s = sentences[i]
markup = pyConText.ConTextMarkup()
markup.setRawText(s.lower())
markup.cleanText()
markup.markItems(modifiers, mode="modifier")
markup.markItems(targets, mode="target")
markup.applyModifiers()
markup.pruneMarks()
markup.pruneSelfModifyingRelationships()
markup.dropInactiveModifiers()
foundTargets = [
n[0] for n in markup.nodes(data=True)
if n[1].get("category", "") == 'target'
]
