def test_parent_section_duplicate_sections_different_parents(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([
{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
},
{
"section_title": "allergies",
"pattern": "Allergies:"
},
{
"section_title": "explanation",
"pattern": "Explanation:",
"parents": ["past_medical_history", "allergies"],
},
])
text = "Past Medical History: some other text. Explanation: The patient has one. Allergies: peanuts Explanation: pt cannot eat peanuts"
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 4
_, _, pmh_parent, _ = doc._.sections[0]
_, _, explanation_parent, _ = doc._.sections[1]
_, _, allergies_parent, _ = doc._.sections[2]
_, _, explanation_parent2, _ = doc._.sections[3]
assert pmh_parent is None
assert explanation_parent == "past_medical_history"
assert allergies_parent is None
assert explanation_parent2 == "allergies"
def test_parent_section_chain_backtracking(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([
{
"section_title": "s1",
"pattern": "section 1:"
},
{
"section_title": "s2",
"pattern": "section 2:",
"parents": ["s1"],
},
{
"section_title": "s3",
"pattern": "section 3:",
"parents": ["s2"],
},
{
"section_title": "s4",
"pattern": "section 4:",
"parents": ["s1"],
},
])
text = "section 1: abc section 2: abc section 3: abc section 4: abc"
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 4
_, _, s1, _ = doc._.sections[0]
_, _, s2, _ = doc._.sections[1]
_, _, s3, _ = doc._.sections[2]
_, _, s4, _ = doc._.sections[3]
assert s1 is None
assert s2 == "s1"
assert s3 == "s2"
assert s4 == "s1"
def test_list_pattern_match(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([{
"section_title":
"past_medical_history",
"pattern": [
{
"LOWER": "past"
},
{
"LOWER": "medical"
},
{
"LOWER": "history"
},
{
"LOWER": ":"
},
],
}])
doc = nlp("Past Medical History: PE")
sectionizer(doc)
(section_title, header, parent, section) = doc._.sections[0]
assert section_title == "past_medical_history"
assert header.text == "Past Medical History:"
assert section.text == "Past Medical History: PE"
def test_add(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([{
"section_title": "section",
"pattern": "my pattern"
}])
assert sectionizer.patterns
def test_parent_section_no_valid_parent(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([
{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
},
{
"section_title": "allergies",
"pattern": "Allergies:"
},
{
"section_title": "explanation",
"pattern": "Explanation:",
"parents": ["past_medical_history"],
},
])
text = "Past Medical History: some other text. Allergies: peanuts Explanation: pt cannot eat peanuts"
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 3
_, _, pmh_parent, _ = doc._.sections[0]
_, _, allergies_parent, _ = doc._.sections[1]
_, _, explanation_parent2, _ = doc._.sections[2]
assert pmh_parent is None
assert allergies_parent is None
assert explanation_parent2 is None
def test_end_line(self):
sectionizer = Sectionizer(nlp, patterns=None, require_end_line=True)
sectionizer.add([{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
}])
text = "\n\n Past Medical History:\n The patient has a Past Medical History: this"
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 2
def test_string_match(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([{
"section_title": "past_medical_history",
"pattern": "Past Medical History:"
}])
doc = nlp("Past Medical History: PE")
sectionizer(doc)
(section_title, header, section) = doc._.sections[0]
assert section_title == "past_medical_history"
assert header.text == "Past Medical History:"
assert section.text == "Past Medical History: PE"
def test_max_scope(self):
sectionizer = Sectionizer(nlp, patterns=None, max_scope=2)
sectionizer.add([{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
}])
doc = nlp("Past Medical History: This is the sentence.")
sectionizer(doc)
title, header, parent, section = doc._.sections[0]
assert (section[len(header) - 1 +
2]._.section_title == "past_medical_history")
assert section[len(header) - 1 + 3]._.section_title is None
def test_num_sections(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
}])
doc = nlp("Past Medical History: PE")
sectionizer(doc)
assert len(doc._.sections) == 1
# Now reprocess and make sure it resets
doc = nlp("Past Medical History: PE")
sectionizer(doc)
assert len(doc._.sections) == 1
def test_named_tuple(self):
doc = nlp("Past Medical History: PE")
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
}])
sectionizer(doc)
section_tup = doc._.sections[0]
from clinical_sectionizer.sectionizer import Section
assert isinstance(section_tup, (tuple, Section))
assert len(section_tup) == 4
(section_title, header, parent, section) = section_tup
assert section_title is section_tup.section_title
assert header is section_tup.section_header
assert parent is section_tup.section_parent
assert section is section_tup.section_span
def test_document_starts_no_header(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
}])
doc = nlp("This is separate. Past Medical History: PE")
sectionizer(doc)
assert len(doc._.sections) == 2
(section_title, header, parent, section_span) = doc._.sections[0]
assert section_title is None
assert header is None
assert section_span.text == "This is separate."
(section_title, header, parent, section_span) = doc._.sections[1]
assert section_title == "past_medical_history"
assert header.text == "Past Medical History:"
assert section_span.text == "Past Medical History: PE"
def test_parent_section_parent_required(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([
{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
},
{
"section_title": "explanation",
"pattern": "Explanation:",
"parents": ["past_medical_history"],
"parent_required": True,
},
])
text = "other text Explanation: The patient has one"
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 1
name, text, parent, section = doc._.sections[0]
assert name is None
assert parent is None
def test_parent_section_multiple_candidates(self):
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([
{
"section_title": "past_medical_history",
"pattern": "Past Medical History:",
},
{
"section_title": "explanation",
"pattern": "Explanation:",
"parents": ["past_medical_history", "allergies"],
},
])
text = "Past Medical History: some other text. Explanation: The patient has one"
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 2
_, _, pmh_parent, _ = doc._.sections[0]
_, _, explanation_parent, _ = doc._.sections[1]
assert pmh_parent is None
assert explanation_parent == "past_medical_history"
def test_duplicate_parent_definitions(self):
with warnings.catch_warnings(record=True) as w:
sectionizer = Sectionizer(nlp, patterns=None)
sectionizer.add([
{
"section_title": "s1",
"pattern": "section 1:"
},
{
"section_title": "s2",
"pattern": "section 2:",
"parents": ["s1"],
},
{
"section_title": "s2",
"pattern": "section 2:",
"parents": ["s3"],
},
{
"section_title": "s3",
"pattern": "section 3:"
},
])
text = (
"section 1: abc section 2: abc section 3: abc section 2: abc")
doc = nlp(text)
sectionizer(doc)
assert len(doc._.sections) == 4
_, _, s1, _ = doc._.sections[0]
_, _, s2, _ = doc._.sections[1]
_, _, s3, _ = doc._.sections[2]
_, _, s2_2, _ = doc._.sections[3]
assert len(w) == 1
assert issubclass(w[0].category, RuntimeWarning)
assert s1 is None
assert s2 == "s1"
assert s3 is None
assert s2_2 == "s3"
def test_initiate(self):
assert Sectionizer(nlp)
def test_load_default_rules(self):
sectionizer = Sectionizer(nlp, patterns="default")
assert sectionizer.patterns
def test_load_no_rules(self):
sectionizer = Sectionizer(nlp, patterns=None)
assert sectionizer.patterns == []