def test_on_modifies_false(self):
def on_modifies(target, modifier, span_between):
return False
context = ConTextComponent(nlp, rules=None)
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
on_modifies=on_modifies)
context.add([item])
doc = nlp("There is no evidence of pneumonia or chf.")
doc.ents = (doc[5:6], doc[7:8])
context(doc)
for ent in doc.ents:
assert len(ent._.modifiers) == 0
def test_not_remove_modifiers_overlap_target(self):
"""Test that a modifier which overlaps with a target is not pruned but does not modify itself."""
doc = nlp("The patient has heart failure.")
doc.ents = (Span(doc, 3, 5, "CONDITION"), )
context_item = ConTextItem("failure", "MODIFIER")
tag_object = TagObject(context_item, 4, 5, doc)
graph = ConTextGraph(remove_overlapping_modifiers=False)
graph.modifiers = [tag_object]
graph.targets = doc.ents
graph.prune_modifiers()
graph.apply_modifiers()
assert overlap_target_modifiers(tag_object.span, doc.ents[0])
assert len(graph.modifiers) == 1
def test_on_modifies_arg_types(self):
def check_arg_types(target, modifier, span_between):
for arg in (target, modifier, span_between):
if not isinstance(arg, spacy.tokens.Span):
return False
return True
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
on_modifies=check_arg_types)
doc = nlp("There is no evidence of pneumonia or chf.")
doc.ents = (doc[5:6], doc[7:8])
tag = TagObject(item, 2, 5, doc)
assert tag.modifies(doc.ents[0]) is True
def test_max_scope_none(self):
"""Test that if max_scope is not None it will reduce the range
of text which is modified.
"""
doc = self.create_num_target_examples()
assert len(doc.ents) == 3
item = ConTextItem("vs",
category="UNCERTAIN",
rule="BIDIRECTIONAL",
max_scope=None)
tag_object = TagObject(item, 5, 6, doc)
for target in doc.ents:
if tag_object.modifies(target):
tag_object.modify(target)
assert tag_object.num_targets == 3
def test_custom_attributes_value1(self):
custom_attrs = {
"NEGATED_EXISTENCE": {
"is_negated": True
},
}
try:
Span.set_extension("is_negated", default=False)
except:
pass
context = ConTextComponent(nlp, add_attrs=custom_attrs)
context.add(
[ConTextItem("no evidence of", "NEGATED_EXISTENCE", "FORWARD")])
doc = nlp("There is no evidence of pneumonia.")
doc.ents = (doc[-2:-1], )
context(doc)
assert doc.ents[0]._.is_negated is True
def test_on_modifies_arg_values(self):
def check_arg_types(target, modifier, span_between):
if target.lower_ != "chf":
return False
if modifier.lower_ != "no evidence of":
return False
if span_between.lower_ != "pneumonia or":
return False
return True
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
on_modifies=check_arg_types)
doc = nlp("There is no evidence of pneumonia or chf.")
doc.ents = (doc[5:6], doc[7:8])
tag = TagObject(item, 2, 5, doc)
assert tag.modifies(doc.ents[1]) is True
def test_max_targets_none(self):
"""Check that if max_targets is None it will not reduce the targets
to the two closest ents.
"""
doc = self.create_num_target_examples()
assert len(doc.ents) == 3
item = ConTextItem("vs",
category="UNCERTAIN",
rule="BIDIRECTIONAL",
max_targets=None)
# Set "vs" to be the modifier
tag_object = TagObject(item, 5, 6, doc)
for target in doc.ents:
tag_object.modify(target)
assert tag_object.num_targets == 3
tag_object.reduce_targets()
assert tag_object.num_targets == 3
def test_max_targets_less_than_targets(self):
"""Check that if max_targets is not None it will reduce the targets
to the two closest ents.
"""
doc = self.create_num_target_examples()
assert len(doc.ents) == 3
item = ConTextItem("vs",
category="UNCERTAIN",
rule="BIDIRECTIONAL",
max_targets=2)
# Set "vs" to be the modifier
tag_object = TagObject(item, 5, 6, doc)
for target in doc.ents:
tag_object.modify(target)
assert tag_object.num_targets == 3
tag_object.reduce_targets()
assert tag_object.num_targets == 2
for target in tag_object._targets:
assert target.lower_ in ("pneumonia", "copd")
def test_simple_callback(self, capsys):
context = ConTextComponent(nlp, rules=None)
def simple_callback(matcher, doc, i, matches):
match_id, start, end = matches[i]
span = doc[start:end]
print("Matched on span:", span)
context.add([
ConTextItem(
"no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
on_match=simple_callback,
)
])
doc = nlp("There is no evidence of pneumonia.")
context(doc)
captured = capsys.readouterr()
assert captured.out == "Matched on span: no evidence of\n"
def test_from_json(self, from_json_file):
assert ConTextItem.from_json(from_json_file)
def test_to_dict(self):
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
item = ConTextItem(literal, category, rule)
assert isinstance(item.to_dict(), dict)
def test_custom_patterns_list(self):
"""Test that rules are loaded from a list"""
item = ConTextItem("evidence of", "DEFINITE_EXISTENCE", "forward")
context = ConTextComponent(nlp, rules="other", rule_list=[item])
assert context.item_data
def test_instantiate1(self):
literal = "no evidence of"
category = "DEFINITE_NEGATED_EXISTENCE"
rule = "forward"
assert ConTextItem(literal, category, rule)
def test_from_dict(self):
d = dict(literal="reason for examination",
category="INDICATION",
rule="FORWARD")
assert ConTextItem.from_dict(d)
def test_limit_scope(self):
"""Test that a 'TERMINATE' TagObject limits the scope of the tag object"""
doc, item, tag_object = self.create_objects()
item2 = ConTextItem("but", "TERMINATE", "TERMINATE")
tag_object2 = TagObject(item2, 2, 4, doc)
assert tag_object.limit_scope(tag_object2)
def test_custom_rules_match(self):
item = ConTextItem("no evidence of", "NEGATED_EXISTENCE", "forward")
context = ConTextComponent(nlp, rules="other", rule_list=[item])
matcher = context.phrase_matcher
assert matcher(nlp("no evidence of"))
def test_default_terminate(self):
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
terminated_by=None)
assert item.terminated_by == set()
def test_limit_scope2(self):
doc, item, tag_object = self.create_objects()
item2 = ConTextItem("but", "TERMINATE", "TERMINATE")
tag_object2 = TagObject(item2, 2, 4, doc)
assert not tag_object2.limit_scope(tag_object)
def test_custom_terminate(self):
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
terminated_by={"POSITIVE_EXISTENCE"})
assert item.terminated_by == {"POSITIVE_EXISTENCE"}
