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CU-869475m5q: Fix tests: add necessary per model CUI sets where appli…
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…cable
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@mart-r
mart-r committed Apr 3, 2024
1 parent ac762c5 commit 38bb6fb
Showing 1 changed file with 114 additions and 15 deletions.
129 changes: 114 additions & 15 deletions medcat/compare_models/tests/test_compare_annotations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,16 @@
import unittest


# helper class for substituting @classmethod and @property
# this is needed because this functionality is deprecated
# in python3.11 and will be removed in 3.13
class classproperty:
def __init__(self, func):
self.fget = func
def __get__(self, instance, owner):
return self.fget(owner)


class ResultsTallyTests(unittest.TestCase):
common = {"type_ids": ["T1"], "detected_name": "NOT IMPORTANT", 'acc': 1.0}
cui2name = {"C1": "Concept 1",
Expand Down Expand Up @@ -112,17 +122,50 @@ def test_21(self):
# START the annotation comparison


def _find_cuis(d: dict, target: str = "cui") -> set:
results = set()
for k, v in d.items():
if k == target:
results.add(v)
elif isinstance(v, dict):
results.update(_find_cuis(v))
return results


def _get_cuis(cls, start_char: str = "d") -> set:
attr_names = [attr for attr in dir(cls) if attr.startswith(start_char)]
all_cuis = set()
for attr in attr_names:
dict_value = getattr(cls, attr)
if not isinstance(dict_value, dict):
# NOTE: most of those will be methods
# in the base unittest.TestCase class,
# e.g doClassCleanups
continue
# find recursively all "cui" values in dict
all_cuis.update(_find_cuis(dict_value))
return all_cuis


class NoOverlapFarAwaySameCUITests(unittest.TestCase):
FIRST = compare_annotations.AnnotationComparisonType.FIRST_HAS
SECOND = compare_annotations.AnnotationComparisonType.SECOND_HAS
d1 = {"start": 10, "end": 15, "cui": 'C1'}
d2 = {"start": 20, "end": 25, "cui": 'C1'}

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls)

def setUp(self) -> None:
self.c12 = compare_annotations.AnnotationComparisonType.determine(self.d1, self.d2,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.c21 = compare_annotations.AnnotationComparisonType.determine(self.d2, self.d1,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)

def test_1st_has_12(self):
self.assertIs(self.c12, self.FIRST)
Expand All @@ -146,11 +189,19 @@ class PartialOverlapSameCUITests(unittest.TestCase):
d2 = {"start": 15, "end": 25, "cui": 'C1'}
expect_identical_cui = True

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls)

def setUp(self) -> None:
self.c12 = compare_annotations.AnnotationComparisonType.determine(self.d1, self.d2,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.c21 = compare_annotations.AnnotationComparisonType.determine(self.d2, self.d1,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.expected = self.SAME_CONCEPT if self.expect_identical_cui else self.DIFF_CONCEPT

def test_partial_12(self):
Expand All @@ -176,11 +227,19 @@ class IdenticalOverlapSameCUITests(unittest.TestCase):
d2 = {"start": 10, "end": 20, "cui": 'C1'}
expect_identical_cui = True

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls)

def setUp(self) -> None:
self.c12 = compare_annotations.AnnotationComparisonType.determine(self.d1, self.d2,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.c21 = compare_annotations.AnnotationComparisonType.determine(self.d2, self.d1,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.expected = self.SAME if self.expect_identical_cui else self.DIFF

def test_identical_12(self):
Expand Down Expand Up @@ -208,11 +267,19 @@ class OverLapOneLargerSameConceptTests(unittest.TestCase):
d2 = {"start": 10, "end": 20, "cui": 'C1'}
expect_identical_cui = True

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls)

def setUp(self) -> None:
self.c12 = compare_annotations.AnnotationComparisonType.determine(self.d1, self.d2,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.c21 = compare_annotations.AnnotationComparisonType.determine(self.d2, self.d1,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.expected_12 = self.L1_SC if self.expect_identical_cui else self.L1_DC
self.expected_21 = self.L2_SC if self.expect_identical_cui else self.L2_DC

Expand Down Expand Up @@ -243,9 +310,15 @@ class PerDocAnnotationSameTests(unittest.TestCase):
d2 = d
expected = compare_annotations.AnnotationComparisonType.IDENTICAL

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls)

def test_all_same(self):
pdad = compare_annotations.PerDocAnnotationDifferences.get(self.d1, self.d2,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.assertEqual(len(pdad.nr_of_comparisons), 1)
for el in compare_annotations.AnnotationComparisonType:
with self.subTest(f"{el}"):
Expand Down Expand Up @@ -346,14 +419,22 @@ class PerDocAnnotatingUnevenLengthsComplicatedTests(unittest.TestCase):
expected21 = {compare_annotations.AnnotationComparisonType.IDENTICAL: 2,
compare_annotations.AnnotationComparisonType.FIRST_HAS: 2}

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls)

def test_has_expected_comparison_12(self):
pdad = compare_annotations.PerDocAnnotationDifferences.get(self.d1, self.d2,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.assertEqual(pdad.nr_of_comparisons, self.expected12)

def test_has_expected_comparison_21(self):
pdad = compare_annotations.PerDocAnnotationDifferences.get(self.d2, self.d1,
pt2ch1=None, pt2ch2=None)
pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
self.assertEqual(pdad.nr_of_comparisons, self.expected21)


Expand All @@ -375,8 +456,14 @@ class PerAnnotationSameDifferencesIdenticalTests(unittest.TestCase):
]
expected_totals = {compare_annotations.AnnotationComparisonType.IDENTICAL: 4}

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls, start_char="annotations")

def setUp(self):
self.pad = compare_annotations.PerAnnotationDifferences(pt2ch1=None, pt2ch2=None)
self.pad = compare_annotations.PerAnnotationDifferences(pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
for nr, ann in enumerate(self.annotations):
self.pad.look_at_doc(ann, ann, f"{nr}")
self.pad.finalise()
Expand Down Expand Up @@ -431,8 +518,14 @@ class PerAnnotationSomeDifferencesIdenticalTests(unittest.TestCase):
comparison_type=compare_annotations.AnnotationComparisonType.SECOND_HAS)),
]

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls, start_char="annotations")

def setUp(self):
self.pad = compare_annotations.PerAnnotationDifferences(pt2ch1=None, pt2ch2=None)
self.pad = compare_annotations.PerAnnotationDifferences(pt2ch1=None, pt2ch2=None,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
for nr, (ann1, ann2) in enumerate(zip(self.annotations1, self.annotations2)):
self.pad.look_at_doc(ann1, ann2, f"{nr}")
self.pad.finalise()
Expand Down Expand Up @@ -527,10 +620,16 @@ class FindsParentsTest(unittest.TestCase):
}},
]

@classproperty
def cuis(cls) -> set:
return _get_cuis(cls, start_char="annotations")

def _set_up_for(self, anns1: list, anns2: list
) -> compare_annotations.PerAnnotationDifferences:
pad = compare_annotations.PerAnnotationDifferences(pt2ch1=self.pt2ch,
pt2ch2=self.pt2ch)
pt2ch2=self.pt2ch,
model1_cuis=self.cuis,
model2_cuis=self.cuis)
for nr, (ann1, ann2) in enumerate(zip(anns1, anns2)):
pad.look_at_doc(ann1, ann2, f"{nr}")
pad.finalise()
Expand Down Expand Up @@ -584,4 +683,4 @@ def test_grandchild_recognised_reverse(self):

def test_great_grandchildren_not_recognised(self):
self.assertCorrectRecognition(self.ggc_reg,
compare_annotations.AnnotationComparisonType.SAME_SPAN_DIFF_CONCEPT)
compare_annotations.AnnotationComparisonType.SAME_SPAN_CONCEPT_NOT_IN_2ND)

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