def test_all_attributes_in_irrelevant_markup_are_false(self):
i_sentence = 'This could possibly be a sign of pneumonia in the lungs.'
i_markup = fc.markup_sentence(i_sentence)
i_classifier = fc.markup_conditions(markup=i_markup)
attributes = list(i_classifier.__dict__.keys())
for a in attributes:
if a not in ['target_values', 'modifiers']:
self.assertFalse(i_classifier.__dict__[a])
def setUp(self):
self.txt = 'There is fluid collection in the abdomen. There is no hematoma near the liver. Evaluate for abscess.'
self.sentenceSpanPairs = helpers.my_sentence_splitter(self.txt)
self.sentences = [x.text for x in self.sentenceSpanPairs]
self.spans = [x.span for x in self.sentenceSpanPairs]
self.modifiers = fc.modifiers
self.targets = fc.targets
self.markups = [fc.markup_sentence(x) for x in self.sentences]
self.document = fc.create_context_doc(self.markups)
def setUp(self):
self.txt = 'There is fluid collection in the abdomen. There is no hematoma near the liver. Evaluate for abscess.'
self.sentenceSpanPairs = helpers.my_sentence_splitter(self.txt)
self.sentences = [x.text for x in self.sentenceSpanPairs]
self.spans = [x.span for x in self.sentenceSpanPairs]
#self.sentences = self.sentences.remove('')
self.modifiers = itemData.instantiateFromCSVtoitemData(
"/Users/alec/Box Sync/Bucher_Surgical_MIMICIII/pyConText_implement/fcFinder/modifiers.tsv"
)
self.targets = itemData.instantiateFromCSVtoitemData(
"file:///Users/alec/Box Sync/Bucher_Surgical_MIMICIII/pyConText_implement/fcFinder/targets.tsv"
)
self.markups = [fc.markup_sentence(x) for x in self.sentences]
self.first_markup = self.markups[0]
self.document = fc.create_context_doc(self.markups)
def setUp(self):
self.txt = 'There is fluid collection in the abdomen. There is no hematoma near the liver. Evaluate for abscess.'
self.sentenceSpanPairs = helpers.my_sentence_splitter(self.txt)
self.sentences = [x.text for x in self.sentenceSpanPairs]
self.spans = [x.span for x in self.sentenceSpanPairs]
self.modifiers = fc.modifiers
self.targets = fc.targets
self.markups = [fc.markup_sentence(x) for x in self.sentences]
self.document = fc.create_context_doc(self.markups)
self.empty_markup = pyConText.ConTextMarkup()
self.first_markup = self.markups[0]
self.second_markup = self.markups[1]
self.third_markup = self.markups[2]
self.first_classifier = fc.markup_conditions(markup=self.first_markup)
self.second_classifier = fc.markup_conditions(
markup=self.second_markup)
self.third_classifier = fc.markup_conditions(markup=self.third_markup)
self.classifier = fc.markup_conditions(markup=self.empty_markup)
def test_indication_with_pseudo_anatomy_is_none(self):
pseudo_sentence = "Evaluate for sternal fluid collection."
pseudo_markup = fc.markup_sentence(pseudo_sentence)
self.assertIsNone(pseudo_markup.markupClass)
def test_indication_with_pseudoanatomy_has_pseudoanatomy(self):
pseudo_sentence = "Evaluate for sternal fluid collection."
pseudo_markup = fc.markup_sentence(pseudo_sentence)
pseudo_conditions = fc.markup_conditions(markup=pseudo_markup)
self.assertTrue(pseudo_conditions.pseudoanatomy)
def test_default_markup_sentence_span_starts_with_zero(self):
self.assertEqual(
fc.markup_sentence(self.sentences[0]).docSpan, self.spans[0])