def test_add_remove_annotation2(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
so.ensure_cache()
len_lookupel2so = len(so.el2so)
len_lookupso2el = len(so.so2el)
for _ in range(5):
so.add_inline(begin=2,
end=3,
tag="vv",
depth=4,
attrib={"resp": "machine"})
for _ in range(5):
to_remove = [it for it in so.standoffs if it.tag == 'vv'][0]
so.remove_inline(to_remove)
self.assertTrue(len_lookupel2so == len(so.el2so))
self.assertTrue(len_lookupso2el == len(so.so2el))
output_xml = etree.tostring(so.text_el).decode("utf-8")
expected_output = "<text><body><p>1 2 3 4 5 6 7 9 10</p><p> 11<lb/> 12 13 14</p></body></text>"
self.assertTrue(output_xml == expected_output)
def test_collapsed_table_1(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
collapsed_table = so.collapsed_table
self.assertTrue(collapsed_table.iloc[0].text == "1 2 3 4 5 6 7 9 10")
self.assertTrue(collapsed_table.iloc[3].text == " 12 13 14")
def test_from_tree_standoff(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
with so.cached_standoff():
self.assertTrue(so.table.iloc[0].context[0].begin == 0)
self.assertTrue(so.table.iloc[-1].context[0].begin == 0)
self.assertTrue(so.table.iloc[0].context[0].end == len(so.plain))
self.assertTrue(so.table.iloc[-1].context[0].end == len(so.plain))
def test_view_1(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
mask = np.zeros(len(so.table), dtype=bool)
mask[10:20] = True
view = standoffconverter.View(so, mask)
self.assertTrue(view.standoff_char_pos(0) == (10, 10))
def test_add_annotation_fail1(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
with self.assertRaises(ValueError):
so.add_inline(begin=17,
end=19,
tag="xx",
depth=3,
attrib={"resp": "machine"})
def test_remove_annotation(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
to_remove = so.standoffs[2]
so.remove_inline(to_remove)
output_xml = etree.tostring(so.text_el).decode("utf-8")
expected_output = '<text><body>1 2 3 4 5 6 7 9 10<p> 11<lb/> 12 13 14</p></body></text>'
self.assertTrue(output_xml == expected_output)
def test_span_2(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
so.ensure_cache()
so.add_span(id="test2", begin=2, end=22, tag="tag2", depth=None)
output_xml = etree.tostring(so.text_el).decode("utf-8")
expected_output = "<text><body><p>1 <tag2Span spanTo=\"test2\"/>2 3 4 5 6 7 9 10</p><p> 11<lb/> <anchor xml_id=\"test2\"/>12 13 14</p></body></text>"
self.assertTrue(output_xml == expected_output)
def test_remove_empty_element(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
to_remove = so.standoffs[-1]
so.remove_inline(to_remove)
output_xml = etree.tostring(so.text_el).decode("utf-8")
expected_out = '''<text><body><p>1 2 3 4 5 6 7 9 10</p><p> 11 12 13 14</p></body></text>'''
self.assertTrue(expected_out == output_xml)
def test_add_empty_element(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
so.add_inline(begin=1, end=1, tag="lb", depth=None, attrib={})
output_xml = etree.tostring(so.text_el).decode("utf-8")
expected_out = '''<text><body><p>1<lb/> 2 3 4 5 6 7 9 10</p><p> 11<lb/> 12 13 14</p></body></text>'''
self.assertTrue(expected_out == output_xml)
def test_add_annotation_1(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
so.add_inline(begin=0,
end=1,
tag="xx",
depth=None,
attrib={"resp": "machine"})
output_xml = etree.tostring(so.text_el).decode("utf-8")
expected_out = '''<text><body><p><xx resp="machine">1</xx> 2 3 4 5 6 7 9 10</p><p> 11<lb/> 12 13 14</p></body></text>'''
self.assertTrue(expected_out == output_xml)
def test_json(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
output_json = so.json
expected_out = '[{"tag": "text", "attrib": {}, "begin": 0, "end": 30, "depth": 0}, {"tag": "body", "attrib": {}, "begin": 0, "end": 30, "depth": 1}, {"tag": "p", "attrib": {}, "begin": 0, "end": 18, "depth": 2}, {"tag": "p", "attrib": {}, "begin": 18, "end": 30, "depth": 2}, {"tag": "lb", "attrib": {}, "begin": 21, "end": 21, "depth": 3}]'
self.assertTrue(expected_out == output_json)
def test_collapsed_table_2(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
collapsed_table = so.collapsed_table
self.assertTrue(str(collapsed_table.iloc[0].context) == "text>body>p")
def test_from_tree_plain(self):
tree = etree.fromstring(input_xml1)
so = standoffconverter.Converter(tree)
with so.cached_standoff():
self.assertTrue(so.plain == '1 2 3 4 5 6 7 9 10 11 12 13 14')