def test_load():
s = biocjson.fromJSON(json.loads(json_str), bioc.SENTENCE)
g = semgraph.load(s)
assert len(g) == 16
assert g.size() == 15
s = bioc.BioCSentence()
g = semgraph.load(s)
assert len(g) == 0
assert g.size() == 0
def detect(self, sentence, locs):
"""
Args:
sentence(BioCSentence): a sentence with universal dependencies
locs(list): a list of (begin, end)
Yields:
(str, MatcherObj, (begin, end)): negation or uncertainty, matcher, matched annotation
"""
try:
g = semgraph.load(sentence)
propagator.propagate(g)
except:
logging.exception(
'Cannot parse dependency graph [offset={}]'.format(
sentence.offset))
raise
else:
if self.sentence_rule and is_neg_graph1(g):
for loc in locs:
yield NEGATION, None, loc
return
for loc in locs:
if self.sentence_rule and is_neg_graph2(g, loc[0], loc[1]):
yield NEGATION, None, loc
for node in find_nodes(g, loc[0], loc[1]):
m = self.match_neg(g, node)
if m:
yield NEGATION, m, loc
m = self.match_uncertainty(g, node)
if m:
yield UNCERTAINTY, m, loc
def graph_detect(self, sentence, locs):
"""Detect rules in report sentences.
Args:
sentence(BioCSentence): a sentence with universal dependencies
locs(list): a list of (begin, end)
Return:
(str, MatcherObj, (begin, end)): negation or uncertainty,
matcher, matched annotation
"""
try:
g = semgraph.load(sentence)
propagator.propagate(g)
except Exception:
logging.exception('Cannot parse dependency graph [offset=%s]',
sentence.offset)
raise
else:
for loc in locs:
for node in find_nodes(g, loc[0], loc[1]):
# Match pre-negation uncertainty rules first.
preneg_m = self.match_prenegation_uncertainty(g, node)
if preneg_m:
yield UNCERTAINTY, preneg_m, loc
else:
# Then match negation rules.
neg_m = self.match_neg(g, node)
if neg_m:
yield NEGATION, neg_m, loc
else:
# Finally match post-negation uncertainty rules.
postneg_m = self.match_uncertainty(g, node)
if postneg_m:
yield UNCERTAINTY, postneg_m, loc
def _read_graph():
s = biocjson.fromJSON(json.loads(json_str), bioc.SENTENCE)
g = semgraph.load(s)
return g
