def test_dir_reader2(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
dir_reader = EhostDirReader(
nlp=English(),
support_overlap=True,
recursive=True,
schema_file='data/ehost_test_corpus/config/projectschema.xml')
docs = dir_reader.read(txt_dir='data/ehost_test_corpus/')
assert (len(docs) == 2)
for doc in docs:
assert (len(doc._.concepts) == 7)
assert ('Doc_Level_Purulence_Assessment' in doc._.concepts)
assert (str(
doc._.concepts['Doc_Level_Purulence_Assessment'][0]) == 'CHIEF'
)
assert ('Purulent' in doc._.concepts)
assert (str(doc._.concepts['Purulent'][0]) == 'Abdominal pain')
assert ('Non-Purulent' in doc._.concepts)
assert (str(doc._.concepts['Non-Purulent'][0]) == 'PRESENT')
assert ('Incision_and_Drainage' in doc._.concepts)
assert (str(
doc._.concepts['Incision_and_Drainage'][0]) == 'patient')
assert ('PreAnnotated' in doc._.concepts)
assert (str(doc._.concepts['PreAnnotated'][0]) == '71-year-old')
assert ('Nonspecific_SSTI' in doc._.concepts)
assert (str(
doc._.concepts['Nonspecific_SSTI'][0]) == 'X. The patient')
assert ('Exclusions' in doc._.concepts)
assert (str(doc._.concepts['Exclusions'][0]) == 'presented')
def test_read(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
ereader = EhostDocReader(
nlp=English(),
schema_file='data/ehost_test_corpus/config/projectschema.xml')
doc = ereader.read('data/ehost_test_corpus/corpus/doc1.txt')
self.eval(doc)
def test_read_doc_name(self):
ereader = EhostDocReader(
nlp=English(),
schema_file='data/ehost_test_corpus/config/projectschema.xml')
doc = ereader.read('data/ehost_test_corpus/corpus/doc1.txt')
assert (doc._.doc_name == 'doc1.txt')
ereader.doc_name_depth = 1
doc = ereader.read('data/ehost_test_corpus/corpus/doc1.txt')
assert (doc._.doc_name == r'corpus/doc1.txt')
ereader = EhostDocReader(
nlp=English(),
schema_file='data/ehost_test_corpus/config/projectschema.xml',
doc_name_depth=2)
doc = ereader.read('data/ehost_test_corpus/corpus/doc1.txt')
assert (doc._.doc_name == r'ehost_test_corpus/corpus/doc1.txt')
def test_parse_to_dicts(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
ereader = EhostDocReader(nlp=English())
spans, classes, attributes, relations = ereader.parse_to_dicts(
'data/ehost_test_corpus/saved/doc1.txt.knowtator.xml')
assert (len(spans) == 7)
assert (len(classes) == 7)
assert (len(attributes) == 6)
def test_set_attributes(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
EhostDocReader(
nlp=English(),
schema_file='data/ehost_test_corpus/config/projectschema.xml')
nlp = English()
doc = nlp('test status attribute')
assert (hasattr(doc[1:2]._, 'status'))
assert (doc[1:2]._.status == 'present')
def test_set_attributes(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
BratDocReader(nlp=English(),
schema_file='data/brat_test_corpus/annotation.conf')
nlp = English()
doc = nlp('test status attribute')
span = doc[1:2]
assert (hasattr(span._, 'Negation'))
assert (hasattr(span._, 'Confidence'))
def test_parse_to_dicts(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
breader = BratDocReader(nlp=English())
spans, classes, attributes, relations = breader.parse_to_dicts(
Path('data/brat_test_corpus/000-introduction.ann').read_text())
assert (len(spans) == 12)
assert (len(classes) == 17)
assert (len(attributes) == 6)
assert (len(relations) == 5)
def test_dir_reader(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
dir_reader = EhostDirReader(
nlp=English(),
recursive=True,
schema_file='data/ehost_test_corpus/config/projectschema.xml')
docs = dir_reader.read(txt_dir='data/ehost_test_corpus/')
assert (len(docs) == 2)
for doc in docs:
self.eval(doc)
def test_check_spans(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
ereader = EhostDocReader(
nlp=English(),
schema_file='data/ehost_test_corpus/config/projectschema.xml',
support_overlap=False,
store_anno_string=True,
encoding='UTF8',
log_level=logging.DEBUG)
doc = ereader.read('data/ehost_test_corpus/corpus/doc2.txt')
for span in doc.ents:
print(span._.span_txt, '<>', span)
assert (span._.span_txt.replace('\n', ' ')
in str(span).replace('\n', ' '))
def remove_doc_extensions():
"""
Remove :mod:`textacy.extract` custom property and method doc extensions
from the global :class:`spacy.tokens.Doc`.
"""
for name in get_doc_extensions().keys():
_ = Doc.remove_extension(name)
def test_check_spans(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
breader = BratDocReader(
nlp=English(),
schema_file='data/brat_test_corpus/annotation.conf',
support_overlap=True,
store_anno_string=True,
encoding='UTF8',
log_level=logging.DEBUG)
doc = breader.read('data/brat_test_corpus/000-introduction.txt')
for span in doc.ents:
if span._.span_txt.replace('\n', ' ') not in str(span).replace(
'\n', ' '):
print(span._.span_txt, '<>', span)
assert (span._.span_txt == 'complicated panic'
or (span._.span_txt.replace('\n', ' ')
in str(span).replace('\n', ' ')))
def test_read(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
breader = BratDocReader(
nlp=English(), schema_file='data/brat_test_corpus/annotation.conf')
doc = breader.read('data/brat_test_corpus/000-introduction.txt')
assert (len(doc.ents) == 12)
assert (str(doc.ents[0].label_) == 'Gene_expression')
assert (str(doc.ents[1].label_) == 'Protein')
assert (str(doc.ents[2].label_) == 'Negative_regulation')
assert (str(doc.ents[3].label_) == 'Positive_regulation')
assert (str(doc.ents[4].label_) == 'Protein')
assert (str(doc.ents[5].label_) == 'Gene_expression')
assert (str(doc.ents[6].label_) == 'Protein')
assert (str(doc.ents[7].label_) == 'Complex')
assert (str(doc.ents[8].label_) == 'Protein')
assert (str(doc.ents[9].label_) == 'Positive_regulation')
assert (str(doc.ents[10].label_) == 'Simple_chemical')
assert (str(doc.ents[11].label_) == 'Protein')
def test_check_spans2(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
breader = BratDocReader(
nlp=English(),
schema_file='data/brat_test_corpus/annotation.conf',
support_overlap=False,
store_anno_string=True,
encoding='UTF8',
log_level=logging.DEBUG)
doc = breader.read(
'data/brat_test_corpus/040-text_span_annotation.txt')
for span in doc.ents:
assert (span._.span_txt.replace('\n', ' ')
in str(span).replace('\n', ' '))
def test_dir_reader(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
dir_reader = BratDirReader(
nlp=English(),
support_overlap=True,
recursive=True,
schema_file='data/brat_test_corpus/annotation.conf')
docs = dir_reader.read(txt_dir='data/brat_test_corpus/')
assert (len(docs) == 2)
doc = docs[0]
assert (len(doc._.concepts) == 6)
assert ('Gene_expression' in doc._.concepts)
assert ('Protein' in doc._.concepts)
assert ('Negative_regulation' in doc._.concepts)
assert ('Positive_regulation' in doc._.concepts)
assert ('Complex' in doc._.concepts)
assert ('Simple_chemical' in doc._.concepts)
assert (len(doc._.concepts['Gene_expression']) == 2)
assert (len(doc._.concepts['Protein']) == 5)
assert (len(doc._.concepts['Negative_regulation']) == 1)
assert (len(doc._.concepts['Positive_regulation']) == 2)
assert (len(doc._.concepts['Complex']) == 1)
assert (len(doc._.concepts['Simple_chemical']) == 1)
def test_dir_reader(self):
if Doc.has_extension("concepts"):
Doc.remove_extension("concepts")
dir_reader = BratDirReader(
nlp=English(),
support_overlap=True,
recursive=True,
schema_file='data/brat_test_corpus/annotation.conf')
docs = dir_reader.read(txt_dir='data/brat_test_corpus/')
assert (len(docs) == 2)
doc = docs[0]
assert (len(doc._.concepts) == 6)
assert ('Gene_expression' in doc._.concepts)
assert ('Protein' in doc._.concepts)
assert ('Negative_regulation' in doc._.concepts)
assert ('Positive_regulation' in doc._.concepts)
assert ('Complex' in doc._.concepts)
assert ('Simple_chemical' in doc._.concepts)
assert (len(doc._.concepts['Gene_expression']) == 2)
assert (len(doc._.concepts['Protein']) == 5)
assert (len(doc._.concepts['Negative_regulation']) == 1)
assert (len(doc._.concepts['Positive_regulation']) == 2)
assert (len(doc._.concepts['Complex']) == 1)
assert (len(doc._.concepts['Simple_chemical']) == 1)
