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")
rule = ConTextRule("no evidence of", "DEFINITE_NEGATED_EXISTENCE",
"FORWARD")
rule2 = ConTextRule("neg for", "DEFINITE_NEGATED_EXISTENCE", "FORWARD")
modifier = ConTextModifier(rule, 0, 3, doc)
modifier2 = ConTextModifier(rule2, 5, 7, doc)
assert modifier.limit_scope(modifier2)
def test_from_dict_error(self):
d = dict(
literal="reason for examination",
category="INDICATION",
direction="FORWARD",
invalid="this is an invalid key",
)
with pytest.raises(ValueError):
ConTextRule.from_dict(d)
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")
rule = ConTextRule("is ruled out", "NEGATED_EXISTENCE", "BACKWARD")
modifier = ConTextModifier(rule, 6, 8, doc)
rule2 = ConTextRule("but", "TERMINATE", "TERMINATE")
modifier2 = ConTextModifier(rule2, 3, 4, doc)
assert modifier.limit_scope(modifier2)
def test_terminate_stops_forward_modifier(self):
context = ConTextComponent(nlp, rules=None)
rule = ConTextRule("no evidence of", "NEGATED_EXISTENCE", "FORWARD")
rule2 = ConTextRule("but", "TERMINATE", "TERMINATE")
context.add([rule, rule2])
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)
rule = ConTextRule("is ruled out", "NEGATED_EXISTENCE", "BACKWARD")
rule2 = ConTextRule("but", "CONJ", "TERMINATE")
context.add([rule, rule2])
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_prune_false(self):
rules = [
ConTextRule("history of", "HISTORICAL", direction="FORWARD"),
ConTextRule("no history of",
"NEGATED_EXISTENCE",
direction="FORWARD"),
]
context = ConTextComponent(nlp, rules=None, prune=False)
context.add(rules)
doc = nlp("No history of afib.")
context(doc)
assert len(doc._.context_graph.modifiers) == 2
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.")
rule = ConTextRule("negative",
"NEGATED_EXISTENCE",
direction="BACKWARD")
rule2 = ConTextRule("positive",
"POSITIVE_EXISTENCE",
direction="BACKWARD",
terminated_by={"NEGATED_EXISTENCE"})
modifier = ConTextModifier(rule, 2, 3, doc)
modifier2 = ConTextModifier(rule2, 6, 7, doc)
assert modifier2.limit_scope(modifier)
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.")
rule = ConTextRule("negative for",
"NEGATED_EXISTENCE",
direction="FORWARD",
terminated_by={"POSITIVE_EXISTENCE"})
rule2 = ConTextRule("positive for",
"POSITIVE_EXISTENCE",
direction="FORWARD")
modifier = ConTextModifier(rule, 0, 2, doc)
modifier2 = ConTextModifier(rule2, 4, 6, doc)
assert modifier.limit_scope(modifier2)
def load():
import medspacy
nlp = medspacy.load(enable=["sentencizer", "tokenizer"])
# Add components
from medspacy.target_matcher import TargetMatcher, TargetRule
target_matcher = TargetMatcher(nlp)
target_filepath = path.join(RESOURCES_DIR, "target_rules.json")
target_rules = TargetRule.from_json(target_filepath)
target_matcher.add(target_rules)
nlp.add_pipe(target_matcher)
from medspacy.context import ConTextComponent, ConTextRule
context_filepath = path.join(RESOURCES_DIR, "context_rules.json")
context = ConTextComponent(nlp, rules=None, add_attrs=CONTEXT_ATTRS)
context_rules = ConTextRule.from_json(context_filepath)
context.add(context_rules)
nlp.add_pipe(context)
from medspacy.section_detection import Sectionizer
# TODO: Add radiology section rules
sectionizer = Sectionizer(nlp)
nlp.add_pipe(sectionizer)
clf = DocumentClassifier(nlp)
nlp.add_pipe(clf)
return nlp
def test_metadata(self):
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
meta = {"comment": "This is a comment."}
item = ConTextRule(literal, category, rule, metadata=meta)
assert item.metadata
def test_rule_value_error(self):
"""Test that ConTextRule raises a ValueError if an invalid direction is passed in."""
literal = "no evidence of"
category = "definite_negated_existence"
rule = "asdf"
with pytest.raises(ValueError):
ConTextRule(literal, category, rule)
def test_context_item_rule_upper(self):
"""Test that a ConTextRule direction is always upper"""
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
item = ConTextRule(literal, category, rule)
assert item.direction == "FORWARD"
def test_context_item_category_upper(self):
"""Test that a ConTextRule category is always upper"""
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
item = ConTextRule(literal, category, rule)
assert item.category == "DEFINITE_NEGATED_EXISTENCE"
def test_custom_terminate_stops_forward_modifier(self):
doc = nlp("negative for flu, positive for pneumonia.")
context = ConTextComponent(nlp, rules=None)
rule = ConTextRule("negative for",
"NEGATED_EXISTENCE",
direction="FORWARD",
terminated_by={"POSITIVE_EXISTENCE"})
rule2 = ConTextRule("positive for",
"POSITIVE_EXISTENCE",
direction="FORWARD")
context.add([rule, rule2])
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_rule_modifier_termination(self):
context = ConTextComponent(nlp, rules=None, terminations=None)
rule = ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
terminated_by={"POSITIVE_EXISTENCE", "UNCERTAIN"})
context.add([rule])
assert rule.terminated_by == {"POSITIVE_EXISTENCE", "UNCERTAIN"}
def test_null_modifier_termination(self):
context = ConTextComponent(nlp, rules=None, terminations=None)
rule = ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
terminated_by=None)
context.add([rule])
assert rule.terminated_by == set()
def create_objects(self):
doc = nlp(
"family history of breast cancer but no diabetes. She has afib.")
rule = ConTextRule("family history of",
"FAMILY_HISTORY",
direction="FORWARD")
modifier = ConTextModifier(rule, 0, 3, doc)
return doc, rule, modifier
def test_is_historical(self):
doc = nlp("History of pneumonia.")
context = ConTextComponent(nlp, add_attrs=True, rules=None)
rules = [ConTextRule("history of", "HISTORICAL", direction="forward")]
context.add(rules)
doc.ents = (doc[-2:-1], )
context(doc)
assert doc.ents[0]._.is_historical is True
def test_pseudo_modifier(self):
rules = [
ConTextRule("negative", "NEGATED_EXISTENCE"),
ConTextRule("negative attitude",
"PSEUDO_NEGATED_EXISTENCE",
direction="PSEUDO"),
]
context = ConTextComponent(nlp, rules=None)
context.add(rules)
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_to_json(self):
import json, os
dname = os.path.join(tmpdirname.name, "test_modifiers.json")
literal = "no evidence of"
category = "definite_negated_existence"
rule = "forward"
item = ConTextRule(literal, category, rule)
ConTextRule.to_json([item], dname)
with open(dname) as f:
data = json.load(f)
assert "context_rules" in data
assert len(data["context_rules"]) == 1
item = data["context_rules"][0]
for key in ["literal", "category", "direction"]:
assert key in item
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.")
rule = ConTextRule("family history of",
"FAMILY_HISTORY",
direction="FORWARD",
max_scope=2)
modifier = ConTextModifier(rule, 0, 3, doc, _use_context_window=True)
assert modifier.scope == doc[3:5]
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 = ConTextRule(
"no evidence of", "DEFINITE_NEGATED_EXISTENCE", "forward"
)
tag_object1 = ConTextModifier(item_data1, 2, 5, doc)
item_data2 = ConTextRule("evidence of", "DEFINITE_EXISTENCE", "forward")
tag_object2 = ConTextModifier(item_data2, 3, 5, doc)
item_data3 = ConTextRule("but", "TERMINATE", "TERMINATE")
tag_object3 = ConTextModifier(item_data3, 6, 7, doc)
graph = ConTextGraph()
graph.modifiers = [tag_object1, tag_object2, tag_object3]
return doc, graph
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.")
rule = ConTextRule("r/o", "UNCERTAIN", direction="BIDIRECTIONAL")
modifier = ConTextModifier(rule, 3, 4, doc)
target = Span(doc, 3, 4, "TEST")
assert modifier.modifies(target) is False
def test_is_family(self):
doc = nlp("Family history of breast cancer.")
context = ConTextComponent(nlp, add_attrs=True, rules=None)
rules = [
ConTextRule("family history of", "FAMILY", direction="forward")
]
context.add(rules)
doc.ents = (doc[-3:-1], )
context(doc)
assert doc.ents[0]._.is_family is True
def test_on_modifies_true(self):
def on_modifies(target, modifier, span_between):
return True
rule = ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
on_modifies=on_modifies)
doc = nlp("There is no evidence of pneumonia or chf.")
doc.ents = (Span(doc, 5, 6, "CONDITION"), Span(doc, 6, 8, "CONDITION"))
mod = ConTextModifier(rule, 2, 5, doc)
assert mod.modifies(doc.ents[0]) is True
def test_global_allowed_types2(self):
"""Check that if the ConTextComponent does not have allowed_types defined
and a ConTextRule does, the ConTextRule will not receive the component's
value.
"""
context = ConTextComponent(nlp, rules=None, allowed_types=None)
rule = ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"PROBLEM"})
context.add([rule])
assert rule.allowed_types == {"PROBLEM"}
def test_no_limit_scope_same_category_different_allowed_types(self):
"""Test that a two ConTextModifiers of the same type but with different
allowed types does not limits the scope of the modifier object.
"""
doc = nlp("no history of travel to Puerto Rico, neg for pneumonia")
rule = ConTextRule(
"no history of",
"DEFINITE_NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"TRAVEL"},
)
rule2 = ConTextRule(
"neg for",
"DEFINITE_NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"CONDITION"},
)
modifier = ConTextModifier(rule, 0, 3, doc)
modifier2 = ConTextModifier(rule2, 8, 10, doc)
assert not modifier.limit_scope(modifier2)
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.")
rule = ConTextRule("family history of",
"FAMILY_HISTORY",
direction="FORWARD")
with pytest.raises(ValueError) as exception_info:
# This should fail because doc.sents are None
ConTextModifier(rule, 0, 3, doc)
exception_info.match(
"ConText failed because sentence boundaries have not been set")
def test_on_modifies_false(self):
def on_modifies(target, modifier, span_between):
return False
rule = ConTextRule("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])
modifier = ConTextModifier(rule, 2, 5, doc)
assert modifier.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()
rule = ConTextRule(
"no history of travel to",
category="DEFINITE_NEGATED_EXISTENCE",
direction="FORWARD",
)
modifier = ConTextModifier(rule, 0, 5, doc)
modifier.set_scope()
travel, condition = doc.ents # "puerto rico", "pneumonia"
assert modifier.modifies(travel) is True
assert modifier.modifies(condition) is True