def setUp(self):
self.empty_sa = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "valid_sa_file1.xml"))
self.has_overlap_sa = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "has_overlap1.xml"))
self.no_overlap_sa = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "no_overlap1.xml"))
class TestPhiWithinRange(unittest.TestCase):
def setUp(self):
self.has_overlap_sa = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "has_overlap1.xml"))
def test_returns_all_phi_for_entire_document_range(self):
all_phi_maybe = phi_within_range(self.has_overlap_sa, 0,
len(self.has_overlap_sa.text))
self.assertEqual(all_phi_maybe, self.has_overlap_sa.get_phi())
class TestSaFilterByPhiAttrs(unittest.TestCase):
def setUp(self):
self.sa1 = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "has_overlap1.xml"))
def test_filtering(self):
# No PHI will have an attribute of foo
self.assertEqual(sa_filter_by_phi_attrs(self.sa1, {"foo": "bar"}), [])
# No filters should be the same as all the PHI
self.assertEqual(sa_filter_by_phi_attrs(self.sa1, {}),
self.sa1.get_phi())
# There should only be one PHI with the id P1.
assert (len(sa_filter_by_phi_attrs(self.sa1, {"id": "P1"})) == 1)
def get_sa_from_dir(dirname):
"""Returns a dictionary in the format of:
{"id": <StandoffAnnotation>}
This is determined by finding all filenames within dirname that pass
is_valid_sa_file.
"""
sas = []
for filename in os.listdir(dirname):
filename = os.path.join(dirname, filename)
if is_valid_sa_file(filename):
sas.append(StandoffAnnotation(filename))
return dict(zip([sa.id for sa in sas], sas))
def setUp(self):
self.has_overlap_sa = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "has_overlap1.xml"))
def setUp(self):
self.has_overlap_sa = StandoffAnnotation(
os.path.join(FIXTURES_PATH, "has_overlap1.xml"))
self.document = Document(self.has_overlap_sa.file_name)