def test_limit_scope3(self):
"""Test that two modifiers of the same type limit the scope of the first modifier."""
doc = nlp("no evidence of CHF, neg for pneumonia")
item = ConTextItem("no evidence of", "DEFINITE_NEGATED_EXISTENCE",
"FORWARD")
item2 = ConTextItem("neg for", "DEFINITE_NEGATED_EXISTENCE", "FORWARD")
tag_object = TagObject(item, 0, 3, doc)
tag_object2 = TagObject(item2, 5, 7, doc)
assert tag_object.limit_scope(tag_object2)
def test_terminate_limit_scope_backward(self):
"""Test that a 'TERMINATE' modifier will limit the scope of a 'BACKWARD' modifier.
"""
doc = nlp("Pt has chf but pneumonia is ruled out")
item = ConTextItem("is ruled out", "NEGATED_EXISTENCE", "BACKWARD")
tag_object = TagObject(item, 6, 8, doc)
item2 = ConTextItem("but", "TERMINATE", "TERMINATE")
tag_object2 = TagObject(item2, 3, 4, doc)
assert tag_object.limit_scope(tag_object2)
def test_terminate_stops_forward_modifier(self):
context = ConTextComponent(nlp, rules=None)
item = ConTextItem("no evidence of", "NEGATED_EXISTENCE", "FORWARD")
item2 = ConTextItem("but", "TERMINATE", "TERMINATE")
context.add([item, item2])
doc = nlp("No evidence of chf but she has pneumonia.")
doc.ents = (Span(doc, 3, 4, "PROBLEM"), Span(doc, 7, 8, "PROBLEM"))
context(doc)
chf, pneumonia = doc.ents
assert len(chf._.modifiers) > 0
assert len(pneumonia._.modifiers) == 0
def test_terminate_stops_backward_modifier(self):
context = ConTextComponent(nlp, rules=None)
item = ConTextItem("is ruled out", "NEGATED_EXISTENCE", "BACKWARD")
item2 = ConTextItem("but", "CONJ", "TERMINATE")
context.add([item, item2])
doc = nlp("Pt has chf but pneumonia is ruled out")
doc.ents = (Span(doc, 2, 3, "PROBLEM"), Span(doc, 4, 5, "PROBLEM"))
context(doc)
chf, pneumonia = doc.ents
assert len(chf._.modifiers) == 0
assert len(pneumonia._.modifiers) > 0
def test_terminate_limit_scope_custom2(self):
"""Test that a modifier will be explicitly terminated by a modifier with a category
in terminated_by."""
doc = nlp("flu is negative, pneumonia is positive.")
item = ConTextItem("negative", "NEGATED_EXISTENCE", rule="BACKWARD")
item2 = ConTextItem("positive",
"POSITIVE_EXISTENCE",
rule="BACKWARD",
terminated_by={"NEGATED_EXISTENCE"})
tag_object = TagObject(item, 2, 3, doc)
tag_object2 = TagObject(item2, 6, 7, doc)
assert tag_object2.limit_scope(tag_object)
def test_terminate_limit_scope_custom(self):
"""Test that a modifier will be explicitly terminated by a modifier with a category
in terminated_by."""
doc = nlp("negative for flu, positive for pneumonia.")
item = ConTextItem("negative for",
"NEGATED_EXISTENCE",
rule="FORWARD",
terminated_by={"POSITIVE_EXISTENCE"})
item2 = ConTextItem("positive for",
"POSITIVE_EXISTENCE",
rule="FORWARD")
tag_object = TagObject(item, 0, 2, doc)
tag_object2 = TagObject(item2, 4, 6, doc)
assert tag_object.limit_scope(tag_object2)
def test_metadata(self):
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
meta = {"comment": "This is a comment."}
item = ConTextItem(literal, category, rule, metadata=meta)
assert item.metadata
def test_rule_value_error(self):
"""Test that ConTextItem raises a ValueError if an invalid rule is passed in."""
literal = "no evidence of"
category = "definite_negated_existence"
rule = "asdf"
with pytest.raises(ValueError):
ConTextItem(literal, category, rule)
def test_context_item_category_upper(self):
"""Test that a ConTextItem category is always upper"""
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
item = ConTextItem(literal, category, rule)
assert item.category == "DEFINITE_NEGATED_EXISTENCE"
def test_deprecated_context_item_throws_error(self):
with pytest.raises(NotImplementedError) as exception_info:
# This should fail because context_item throws a NotImplementedError
from medspacy.context import ConTextItem
ConTextItem()
exception_info.match(
"ConTextItem has been deprecated and replaced with ConTextRule.")
def test_context_item_rule_upper(self):
"""Test that a ConTextItem rule is always upper"""
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
item = ConTextItem(literal, category, rule)
assert item.rule == "FORWARD"
def test_custom_terminate_stops_forward_modifier(self):
doc = nlp("negative for flu, positive for pneumonia.")
context = ConTextComponent(nlp, rules=None)
item = ConTextItem("negative for",
"NEGATED_EXISTENCE",
rule="FORWARD",
terminated_by={"POSITIVE_EXISTENCE"})
item2 = ConTextItem("positive for",
"POSITIVE_EXISTENCE",
rule="FORWARD")
context.add([item, item2])
doc.ents = (Span(doc, 2, 3, "PROBLEM"), Span(doc, 6, 7))
flu, pneumonia = doc.ents
context(doc)
assert len(flu._.modifiers) == 1
assert len(pneumonia._.modifiers) == 1
def test_item_modifier_termination(self):
context = ConTextComponent(nlp, rules=None, terminations=None)
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
terminated_by={"POSITIVE_EXISTENCE", "UNCERTAIN"})
context.add([item])
assert item.terminated_by == {"POSITIVE_EXISTENCE", "UNCERTAIN"}
def test_null_modifier_termination(self):
context = ConTextComponent(nlp, rules=None, terminations=None)
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
terminated_by=None)
context.add([item])
assert item.terminated_by == set()
def create_objects(self):
doc = nlp(
"family history of breast cancer but no diabetes. She has afib.")
item = ConTextItem("family history of",
"FAMILY_HISTORY",
rule="FORWARD")
tag_object = TagObject(item, 0, 3, doc)
return doc, item, tag_object
def test_is_historical(self):
doc = nlp("History of pneumonia.")
context = ConTextComponent(nlp, add_attrs=True, rules=None)
item_data = [ConTextItem("history of", "HISTORICAL", rule="forward")]
context.add(item_data)
doc.ents = (doc[-2:-1], )
context(doc)
assert doc.ents[0]._.is_historical is True
def test_pseudo_modifier(self):
item_data = [
ConTextItem("negative", "NEGATED_EXISTENCE"),
ConTextItem("negative attitude",
"PSEUDO_NEGATED_EXISTENCE",
rule="PSEUDO"),
]
context = ConTextComponent(nlp, rules=None)
context.add(item_data)
doc = nlp("She has a negative attitude about her treatment.")
doc.ents = (doc[-2:-1], )
context(doc)
assert len(doc.ents[0]._.modifiers) == 0
assert len(doc._.context_graph.modifiers) == 1
assert doc._.context_graph.modifiers[
0].category == "PSEUDO_NEGATED_EXISTENCE"
def test_set_scope_context_window_no_sentences(self):
"""Test that setting the scope succeeds if sentence boundaries haven't been set but _use_context_window is True."""
doc = nlp.tokenizer(
"family history of breast cancer but no diabetes. She has afib.")
item = ConTextItem("family history of",
"FAMILY_HISTORY",
rule="FORWARD",
max_scope=2)
tag_object = TagObject(item, 0, 3, doc, _use_context_window=True)
assert tag_object.scope == doc[3:5]
def test_overlapping_target(self):
"""Test that a modifier will not modify a target if it is
in the same span as the modifier.
"""
doc = nlp("Pt presents for r/o of pneumonia.")
item = ConTextItem("r/o", "UNCERTAIN", rule="BIDIRECTIONAL")
tag_object = TagObject(item, 3, 4, doc)
target = Span(doc, 3, 4, "TEST")
assert tag_object.modifies(target) is False
def test_is_negated(self):
doc = nlp("There is no evidence of pneumonia.")
context = ConTextComponent(nlp, add_attrs=True, rules=None)
item_data = [
ConTextItem("no evidence of", "NEGATED_EXISTENCE", rule="forward")
]
context.add(item_data)
doc.ents = (doc[-2:-1], )
context(doc)
assert doc.ents[0]._.is_negated is True
def test_is_family(self):
doc = nlp("Family history of breast cancer.")
context = ConTextComponent(nlp, add_attrs=True, rules=None)
item_data = [
ConTextItem("family history of", "FAMILY", rule="forward")
]
context.add(item_data)
doc.ents = (doc[-3:-1], )
context(doc)
assert doc.ents[0]._.is_family is True
def context_graph(self):
doc = nlp.tokenizer(
"There is no evidence of pneumonia but there is chf.")
doc[0].is_sent_start = True
for token in doc[1:]:
token.is_sent_start = False
item_data1 = ConTextItem("no evidence of",
"DEFINITE_NEGATED_EXISTENCE", "forward")
tag_object1 = TagObject(item_data1, 2, 5, doc)
item_data2 = ConTextItem("evidence of", "DEFINITE_EXISTENCE",
"forward")
tag_object2 = TagObject(item_data2, 3, 5, doc)
item_data3 = ConTextItem("but", "TERMINATE", "TERMINATE")
tag_object3 = TagObject(item_data3, 6, 7, doc)
graph = ConTextGraph()
graph.modifiers = [tag_object1, tag_object2, tag_object3]
return doc, graph
def test_set_scope_fails_no_sentences(self):
"""Test that setting the scope fails if sentence boundaries haven't been set."""
doc = nlp.tokenizer(
"family history of breast cancer but no diabetes. She has afib.")
item = ConTextItem("family history of",
"FAMILY_HISTORY",
rule="FORWARD")
with pytest.raises(ValueError) as exception_info:
# This should fail because doc.sents are None
TagObject(item, 0, 3, doc)
exception_info.match(
"ConText failed because sentence boundaries have not been set")
def test_no_limit_scope_same_category_different_allowed_types(self):
"""Test that a two TagObjects of the same type but with different
allowed types does not limits the scope of the tag object.
"""
doc = nlp("no history of travel to Puerto Rico, neg for pneumonia")
item = ConTextItem(
"no history of",
"DEFINITE_NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"TRAVEL"},
)
item2 = ConTextItem(
"neg for",
"DEFINITE_NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"CONDITION"},
)
tag_object = TagObject(item, 0, 3, doc)
tag_object2 = TagObject(item2, 8, 10, doc)
assert not tag_object.limit_scope(tag_object2)
def test_global_allowed_types2(self):
"""Check that if the ConTextComponent does not have allowed_types defined
and a ConTextItem does, the ConTextItem will not receive the component's
value.
"""
context = ConTextComponent(nlp, rules=None, allowed_types=None)
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"PROBLEM"})
context.add([item])
assert item.allowed_types == {"PROBLEM"}
def test_on_modifies_false(self):
def on_modifies(target, modifier, span_between):
return False
item = ConTextItem("no evidence of",
"NEGATED_EXISTENCE",
on_modifies=on_modifies)
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 False
def test_no_types(self):
"""Test that not specifying allowed_types or excluded_types will modify all targets."""
doc = self.create_target_type_examples()
item = ConTextItem(
"no history of travel to",
category="DEFINITE_NEGATED_EXISTENCE",
rule="FORWARD",
)
tag_object = TagObject(item, 0, 5, doc)
tag_object.set_scope()
travel, condition = doc.ents # "puerto rico", "pneumonia"
assert tag_object.modifies(travel) is True
assert tag_object.modifies(condition) is True
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_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_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