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_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 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_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_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_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 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)
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_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_global_allowed_types1(self):
"""Check that if the ConTextComponent has allowed_types defined
and a ConTextRule does not, the ConTextRule will receive the component's
value.
"""
context = ConTextComponent(nlp, rules=None, allowed_types={"PROBLEM"})
rule = ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
allowed_types=None)
context.add([rule])
assert rule.allowed_types == {"PROBLEM"}
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_regex_pattern(self):
rules = [
ConTextRule("no history of",
"NEGATED_EXISTENCE",
direction="FORWARD",
pattern="no (history|hx) of"),
]
context = ConTextComponent(nlp, rules=None)
context.add(rules)
doc = nlp("No history of afib. No hx of MI.")
context(doc)
assert len(doc._.context_graph.modifiers) == 2
def test_global_allowed_types2(self):
"""Check that if both the ConTextComponent and a ConTextRule have allowed_types defined,
the ConTextRule will not receive the component's value.
"""
context = ConTextComponent(nlp,
rules=None,
allowed_types={"TREATMENT"})
rule = ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
"FORWARD",
allowed_types={"PROBLEM"})
context.add([rule])
assert rule.allowed_types == {"PROBLEM"}
def test_is_negated(self):
doc = nlp("There is no evidence of pneumonia.")
context = ConTextComponent(nlp, add_attrs=True, rules=None)
rules = [
ConTextRule("no evidence of",
"NEGATED_EXISTENCE",
direction="forward")
]
context.add(rules)
doc.ents = (Span(doc, 5, 6, "CONDITION"), )
context(doc)
assert doc.ents[0]._.is_negated is True
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_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_custom_patterns_json(self):
"""Test that rules are loaded from a json"""
context = ConTextComponent(
nlp,
rules="other",
rule_list=os.path.abspath("resources/context_rules.json"))
assert context.item_data
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_registers_attributes(self):
"""Test that the default ConText attributes are set on ."""
doc = nlp("There is consolidation.")
doc.ents = (doc[-2:-1], )
context = ConTextComponent(nlp)
doc = context(doc)
assert hasattr(doc._, "context_graph")
assert hasattr(doc.ents[0]._, "modifiers")
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 = (Span(doc, 7, 8, "CONDITION"), )
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_context_window_no_max_scope_fails(self):
"Test that if use_context_window is True but max_scope is None, the instantiation will fail"
with pytest.raises(ValueError) as exception_info:
context = ConTextComponent(nlp,
max_scope=None,
use_context_window=True)
exception_info.match(
"If 'use_context_window' is True, 'max_scope' must be an integer greater 1, not None"
)
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_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_custom_patterns_json(self):
"""Test that rules are loaded from a json"""
if os.path.exists("./resources/context_rules.json"):
filepath = "./resources/context_rules.json"
else:
filepath = "../../resources/context_rules.json"
context = ConTextComponent(nlp,
rules="other",
rule_list=os.path.abspath(filepath))
assert context.rules
def test_custom_attribute_error(self):
"""Test that a custom spacy attribute which has not been set
will throw a ValueError.
"""
custom_attrs = {
"FAKE_MODIFIER": {
"non_existent_attribute": True
},
}
with pytest.raises(ValueError):
ConTextComponent(nlp, add_attrs=custom_attrs)
def test_custom_attributes_value2(self):
custom_attrs = {
"FAMILY": {
"is_family": True
},
}
try:
Span.set_extension("is_family", default=False)
except:
pass
context = ConTextComponent(nlp, add_attrs=custom_attrs)
context.add([
ConTextRule("no evidence of", "DEFINITE_NEGATED_EXISTENCE",
"FORWARD")
])
doc = nlp("There is no evidence of pneumonia.")
doc.ents = (doc[-2:-1], )
context(doc)
assert doc.ents[0]._.is_family is False
def test_custom_attributes_mapping(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)
assert context.context_attributes_mapping == custom_attrs
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"
