def test_union_patterns_empty_test():
filename = 'config/i2b2_2016_track-1.conf'
score_values = ['(Patient|Provider)']
namespaces , document_data , ref_patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
score_values = ['I.Do.No.Exist']
namespaces , document_data , test_patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
ref_patterns , test_patterns = \
args_and_configs.align_patterns( ref_patterns , test_patterns )
for ref_pattern in ref_patterns:
match_flag = False
for test_pattern in test_patterns:
if (test_pattern['type'] == ref_pattern['type']):
match_flag = True
test_pattern['type'] == ref_pattern['type']
break
if (match_flag == False):
assert ref_pattern['type'] == False
for test_pattern in test_patterns:
match_flag = False
for ref_pattern in ref_patterns:
if (test_pattern['type'] == ref_pattern['type']):
match_flag = True
test_pattern['type'] == ref_pattern['type']
break
if (match_flag == False):
assert test_pattern['type'] == False
def test_writing_dictionary_for_datetime_from_0005_gs():
ingest_file = 'tests/data/i2b2_2016_track-1_reference/0005_gs.xml'
reference_file = 'tests/data/i2b2_2016_track-1_reference_out/0005_gs.xml'
config_file = 'config/i2b2_2016_track-1.conf'
try:
tmp_descriptor, tmp_file = tempfile.mkstemp()
os.close(tmp_descriptor)
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
text_extraction.extract_annotations(ingest_file,
namespaces=namespaces,
document_data=document_data,
patterns=patterns,
skip_chars=r'[\s]',
out_file=tmp_file)
with open(reference_file, 'r') as rf:
reloaded_reference = json.load(rf)
with open(tmp_file, 'r') as tf:
reloaded_test = json.load(tf)
assert reloaded_reference['annotations'] == reloaded_test[
'annotations']
assert reloaded_reference['offset_mapping'] == reloaded_test[
'offset_mapping']
assert reloaded_reference['raw_content'] == reloaded_test[
'raw_content']
finally:
os.remove(tmp_file)
def test_extracting_no_optional_attributes():
ingest_file = 'tests/data/013_Conditional_Problem.xmi'
config_file = 'config/webanno_problems_allergies_xmi.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
strict_starts = \
text_extraction.extract_annotations_xml( ingest_file ,
offset_mapping = {} ,
annotation_path = \
'./custom:Problems' ,
tag_name = 'Problem' ,
namespaces = namespaces ,
begin_attribute = 'begin' ,
end_attribute = 'end' ,
optional_attributes = [] )
expected_output = \
{ '181' : [ { 'type': 'Problem' ,
'begin_pos': '181' ,
'end_pos': '188' ,
'raw_text': None } ] ,
'218' : [ { 'type': 'Problem' ,
'begin_pos': '218' ,
'end_pos': '224' ,
'raw_text': None } ]
}
assert strict_starts == expected_output
def test_contents_of_write_of_dictionary_for_brat_patterns():
ingest_file = 'tests/data/brat_reference/problems_and_allergens.ann'
config_file = 'config/brat_problems_allergies_standoff.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
with tempfile.NamedTemporaryFile() as tmpfile_handle:
assert os.path.exists(tmpfile_handle.name)
offset_mapping , strict_starts = \
text_extraction.extract_annotations( ingest_file ,
namespaces = namespaces ,
document_data = document_data ,
patterns = patterns ,
skip_chars = r'[\s]' ,
out_file = tmpfile_handle.name )
reloaded_json = json.load(tmpfile_handle)
assert reloaded_json['annotations'] == strict_starts
## T34 Problem 474 493 shortness of breath
## A1 Negated T34
assert strict_starts['474'][0]['begin_pos'] == '474'
assert strict_starts['474'][0]['end_pos'] == '493'
assert strict_starts['474'][0]['raw_text'] == 'shortness of breath'
assert strict_starts['474'][0]['Historical'] == 'false'
assert strict_starts['474'][0]['Negated'] == 'true'
assert os.path.exists(tmpfile_handle.name)
assert os.path.exists(tmpfile_handle.name) == False
def test_count_ref_set_default(capsys):
presaved_file = 'tests/data/i2b2_2016_track-1_reference_out/0005_gs.xml'
command_line_args = [
'etude.py', '--reference-input',
'tests/data/i2b2_2016_track-1_reference', '--reference-config',
'config/i2b2_2016_track-1.conf', '--print-counts', '--no-metrics'
]
with patch.object(sys, 'argv', command_line_args):
args = etude.init_args()
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = args.reference_config ,
score_key = args.score_key ,
score_values = args.score_values )
with open(presaved_file, 'r') as fp:
reloaded_json = json.load(fp)
etude.count_ref_set(this_ns=namespaces,
this_dd=document_data,
this_patterns=patterns,
this_folder=args.reference_input,
args=args,
file_prefix=args.file_prefix,
file_suffix=args.file_suffix[0])
default_out, err = capsys.readouterr()
expected_values = [['counts', 'n'], ['Total', '482']]
for expected_values in expected_values:
print(args.delim.join('{}'.format(m) for m in expected_values))
expected_out, err = capsys.readouterr()
default_out = default_out.strip()
expected_out = expected_out.strip()
assert default_out == expected_out
def test_count_ref_set_csv_out():
presaved_file = 'tests/data/i2b2_2016_track-1_csv_out.csv'
try:
tmp_descriptor, tmp_file = tempfile.mkstemp()
os.close(tmp_descriptor)
command_line_args = [
'etude.py', '--reference-input',
'tests/data/i2b2_2016_track-1_reference', '--reference-config',
'config/i2b2_2016_track-1.conf', '--csv-out', tmp_file,
'--by-file', '--by-type', '--by-file-and-type',
'--by-type-and-file', '--print-counts', '--no-metrics'
]
with patch.object(sys, 'argv', command_line_args):
args = etude.init_args()
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = args.reference_config ,
score_key = args.score_key ,
score_values = args.score_values )
import csv
with open(presaved_file, 'r') as fp:
reloaded_csv = fp.read()
etude.count_ref_set(this_ns=namespaces,
this_dd=document_data,
this_patterns=patterns,
this_folder=args.reference_input,
args=args,
file_prefix=args.file_prefix,
file_suffix=args.file_suffix[0])
with open(tmp_file, 'r') as fp:
new_csv = fp.read()
assert new_csv == reloaded_csv
finally:
os.remove(tmp_file)
def test_default_document_format():
filename = 'config/i2b2_2016_track-1.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
assert document_data['format'] == 'Unknown'
def test_set_score_key_Sentences():
filename = 'config/uima_sentences.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
for pattern in patterns:
assert pattern['type'] == "Sentence"
def test_plaintext_document_format():
filename = 'config/plaintext_sentences.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
assert document_data['format'] == 'txt'
def test_i2b2_2016_track_1_has_empty_namespace():
config_file = 'config/i2b2_2016_track-1.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
## Empty dictionary resolves as False
assert not bool(namespaces)
def test_skip_missing_XPath():
filename = 'config/i2b2_2016_track-1.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
for pattern in patterns:
assert pattern['long_name'] != "Other Person Name"
def test_raw_content_extraction_from_plaintext():
filename = 'config/plaintext_sentences.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
assert 'cdata_xpath' not in document_data
assert 'tag_xpath' not in document_data
assert 'content_attribute' not in document_data
def test_raw_content_extraction_from_attribute():
filename = 'config/webanno_phi_xmi.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
assert 'cdata_xpath' not in document_data
assert document_data['tag_xpath'] == './cas:Sofa'
assert document_data['content_attribute'] == 'sofaString'
def test_raw_content_extraction_from_cdata():
filename = 'config/i2b2_2016_track-1.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
assert document_data['cdata_xpath'] == './TEXT'
assert 'tag_xpath' not in document_data
assert 'content_attribute' not in document_data
def test_webanno_custom_namespaces():
config_file = 'config/webanno_uima_xmi.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
## Non-empty dictionary resolves as True
expected_namespaces = {'custom': 'http:///webanno/custom.ecore'}
with open('/tmp/stdout.log', 'w') as fp:
fp.write('-----------\n{}\n-------------\n'.format(namespaces))
assert namespaces == expected_namespaces
def test_set_score_key_match_over_multiple_values_Tutorial():
filename = 'config/CAS_XMI.conf'
score_values = ['^D.*e$', '^D.*n$', '^T.*e$']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
for pattern in patterns:
assert pattern['type'] == "DateTime"
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Parent' ,
score_values = score_values )
for pattern in patterns:
assert pattern['type'] == "Time"
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Long Name' ,
score_values = score_values )
for pattern in patterns:
assert pattern['type'] == "Date and Time Information"
def test_set_score_key_match_strict_start_and_end_char_Tutorial():
filename = 'config/CAS_XMI.conf'
score_values = ['^[DT].*[en]$']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
for pattern in patterns:
assert pattern['type'] == "DateTime"
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Parent' ,
score_values = score_values )
for pattern in patterns:
assert pattern['type'] == "Time"
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Long Name' ,
score_values = score_values )
for pattern in patterns:
assert pattern['type'] == "Date and Time Information"
def convert_configs_to_json():
fileroots = [
'CAS_XMI', 'i2b2_2016_track-1', 'uima_sentences', 'webanno_uima_xmi'
]
for fileroot in fileroots:
filename = 'config/' + fileroot + '.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
with open('tests/data/' + fileroot + '.json', 'w') as fp:
json.dump(patterns, fp, indent=4)
def test_sentences_has_defined_namespaces():
config_file = 'config/uima_sentences.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
## Non-empty dictionary resolves as True
expected_namespaces = \
{ 'cas' : 'http:///uima/cas.ecore' ,
'type': 'http:///com/clinacuity/deid/nlp/uima/type.ecore',
'type4': 'http:///de/tudarmstadt/ukp/dkpro/core/api/segmentation/type.ecore'
}
assert namespaces == expected_namespaces
def test_optional_attributes():
filename = 'config/webanno_problems_allergies_xmi.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
assert 'conditional' in patterns[0]['optional_attributes']
assert 'generic' in patterns[0]['optional_attributes']
assert 'historical' in patterns[0]['optional_attributes']
assert 'negated' in patterns[0]['optional_attributes']
assert 'not_patient' in patterns[0]['optional_attributes']
assert 'uncertain' in patterns[0]['optional_attributes']
def test_brat_standoff_format():
filename = 'config/brat_problems_allergies_standoff.conf'
score_values = ['.*']
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = filename ,
score_key = 'Short Name' ,
score_values = score_values )
for pattern in patterns:
assert pattern['short_name'] == 'Problem' or pattern[
'short_name'] == 'Allergen'
assert pattern['type_prefix'] == 'T'
assert pattern['optional_attributes'] == [
'Conditional', 'Generic', 'Historical', 'Negated', 'NotPatient',
'Uncertain'
]
def test_extracting_sentences_from_CTAKES4_OpenNLP1_8():
ingest_file = 'tests/data/sentences/992321-OUT.xmi'
config_file = 'config/uima_sentences.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
strict_starts = \
text_extraction.extract_annotations_xml( ingest_file ,
offset_mapping = {} ,
namespaces = namespaces ,
annotation_path = \
'.//type:Sentence' ,
tag_name = 'Sentence' ,
begin_attribute = 'begin' ,
end_attribute = 'end' )
assert len(strict_starts) == 82
def test_extracting_sentences_from_0005_gs():
ingest_file = 'tests/data/i2b2_2016_track-1_reference/0005_gs.xml'
config_file = 'config/uima_sentences.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
strict_starts = \
text_extraction.extract_annotations_xml( ingest_file ,
offset_mapping = {} ,
namespaces = namespaces ,
annotation_path = \
'.//type:Sentence' ,
tag_name = 'Sentence' ,
begin_attribute = 'begin' ,
end_attribute = 'end' )
assert strict_starts == {}
def test_of_presaved_dictionary_for_complex_patterns():
ingest_file = 'tests/data/i2b2_2016_track-1_reference/0005_gs.xml'
presaved_file = 'tests/data/i2b2_2016_track-1_reference_out/0005_gs.xml'
config_file = 'config/i2b2_2016_track-1.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
with open(presaved_file, 'r') as fp:
reloaded_json = json.load(fp)
offset_mapping , strict_starts = \
text_extraction.extract_annotations( ingest_file ,
namespaces = namespaces ,
document_data = document_data ,
patterns = patterns ,
skip_chars = r'[\s]' ,
out_file = None )
assert reloaded_json['annotations'] == strict_starts
def test_count_ref_set_by_type_and_file(capsys):
presaved_file = 'tests/data/i2b2_2016_track-1_reference_out/0005_gs.xml'
command_line_args = [
'etude.py', '--reference-input',
'tests/data/i2b2_2016_track-1_reference', '--reference-config',
'config/i2b2_2016_track-1.conf', '--by-type', '--by-file',
'--print-counts', '--no-metrics'
]
with patch.object(sys, 'argv', command_line_args):
args = etude.init_args()
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = args.reference_config ,
score_key = args.score_key ,
score_values = args.score_values )
with open(presaved_file, 'r') as fp:
reloaded_json = json.load(fp)
etude.count_ref_set(this_ns=namespaces,
this_dd=document_data,
this_patterns=patterns,
this_folder=args.reference_input,
args=args,
file_prefix=args.file_prefix,
file_suffix=args.file_suffix[0])
default_out, err = capsys.readouterr()
expected_values = [['counts', 'n'], ['Total', '482'],
['0005_gs.xml', '36'], ['0016_gs.xml', '54'],
['0267_gs.xml', '63'], ['0273_gs.xml', '35'],
['0389_gs.xml', '40'], ['0475_gs.xml', '46'],
['0617_gs.xml', '38'], ['0709_gs.xml', '45'],
['0982_gs.xml', '100'], ['0992_gs.xml', '25'],
['Age', '92'], ['DateTime',
'124'], ['HCUnit', '76'],
['OtherGeo', '5'], ['OtherID', '7'],
['OtherOrg', '21'], ['Patient', '19'],
['PhoneFax', '6'], ['Provider', '64'], ['SSN', '0'],
['StateCountry', '33'], ['StreetCity', '29'],
['Zip', '4'], ['eAddress', '2']]
for expected_values in expected_values:
print(args.delim.join('{}'.format(m) for m in expected_values))
expected_out, err = capsys.readouterr()
default_out = default_out.strip()
expected_out = expected_out.strip()
assert default_out == expected_out
def test_of_identity_read_write_of_dictionary_for_complex_patterns():
ingest_file = 'tests/data/i2b2_2016_track-1_reference/0005_gs.xml'
config_file = 'config/i2b2_2016_track-1.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
with tempfile.NamedTemporaryFile() as tmpfile_handle:
assert os.path.exists(tmpfile_handle.name)
offset_mapping , strict_starts = \
text_extraction.extract_annotations( ingest_file ,
namespaces = namespaces ,
document_data = document_data ,
patterns = patterns ,
skip_chars = r'[\s]' ,
out_file = tmpfile_handle.name )
reloaded_json = json.load(tmpfile_handle)
assert reloaded_json['annotations'] == strict_starts
assert os.path.exists(tmpfile_handle.name)
assert os.path.exists(tmpfile_handle.name) == False
def test_empty_contents_of_write_of_dictionary_for_brat_patterns():
ingest_file = 'tests/data/brat_reference/ibm.ann'
config_file = 'config/brat_problems_allergies_standoff.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
with tempfile.NamedTemporaryFile() as tmpfile_handle:
assert os.path.exists(tmpfile_handle.name)
offset_mapping , strict_starts = \
text_extraction.extract_annotations( ingest_file ,
namespaces = namespaces ,
document_data = document_data ,
patterns = patterns ,
skip_chars = r'[\s]' ,
out_file = tmpfile_handle.name )
assert strict_starts == {}
assert os.path.exists(tmpfile_handle.name)
with open(tmpfile_handle.name, 'r') as rf:
reloaded_out_file = json.load(rf)
assert reloaded_out_file["annotations"] == {}
assert reloaded_out_file[
"raw_content"] == "International Business Machines Corporation: IBM is Big Blue\n"
assert os.path.exists(tmpfile_handle.name) == False
def test_extracting_with_and_without_optional_attributes_called_by_parent():
ingest_file = 'tests/data/013_Conditional_Problem.xmi'
config_file = 'config/webanno_problems_allergies_xmi.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
patterns.pop()
offset_mapping , annots_with_opt_attributes = \
text_extraction.extract_annotations( ingest_file ,
namespaces = namespaces ,
document_data = document_data ,
patterns = patterns ,
skip_chars = None ,
out_file = None )
patterns[0]['optional_attributes'] = []
offset_mapping , annots_without_opt_attributes = \
text_extraction.extract_annotations( ingest_file ,
namespaces = namespaces ,
document_data = document_data ,
patterns = patterns ,
skip_chars = None ,
out_file = None )
expected_output_without_opt_attributes = \
{ '181' : [ { 'type': 'Problem' ,
'begin_pos': '181' ,
'end_pos': '188' ,
'raw_text': None } ] ,
'218' : [ { 'type': 'Problem' ,
'begin_pos': '218' ,
'end_pos': '224' ,
'raw_text': None } ]
}
expected_output_with_opt_attributes = \
{ '181' : [ { 'type': 'Problem' ,
'begin_pos': '181' ,
'end_pos': '188' ,
'raw_text': None ,
'conditional' : 'true' ,
'generic' : 'false' ,
'historical' : 'false' ,
'negated' : 'false' ,
'not_patient' : 'true' ,
'uncertain' : 'false' } ] ,
'218' : [ { 'type': 'Problem' ,
'begin_pos': '218' ,
'end_pos': '224' ,
'raw_text': None ,
'conditional' : 'false' ,
'generic' : 'false' ,
'historical' : 'true' ,
'negated' : 'false' ,
'not_patient' : 'false' ,
'uncertain' : 'true' } ]
}
assert annots_with_opt_attributes == \
expected_output_with_opt_attributes
assert annots_without_opt_attributes == \
expected_output_without_opt_attributes
assert annots_with_opt_attributes != \
expected_output_without_opt_attributes
assert annots_without_opt_attributes != \
expected_output_with_opt_attributes
args.test_config, args.test_input, args.test_out, args.score_key,
args.fuzzy_flags
])
return args
if __name__ == "__main__":
##
args = init_args()
## Extract and process the two input file configs
if (args.reference_input):
try:
reference_ns , reference_dd , reference_patterns = \
args_and_configs.process_config( config_file = args.reference_config ,
score_key = args.score_key ,
score_values = args.score_values ,
collapse_all_patterns = args.collapse_all_patterns ,
verbose = args.verbose )
except:
e = sys.exc_info()[0]
log.error(
'Uncaught exception in process_config for reference config: {}'
.format(e))
if (reference_patterns == []):
log.error(
'No reference patterns extracted from config. Bailing out now.'
)
exit(1)
if (args.test_input):
try:
test_ns , test_dd , test_patterns = \
def test_extracting_with_and_without_optional_attributes():
ingest_file = 'tests/data/013_Conditional_Problem.xmi'
config_file = 'config/webanno_problems_allergies_xmi.conf'
namespaces , document_data , patterns = \
args_and_configs.process_config( config_file = config_file ,
score_key = 'Short Name' ,
score_values = [ '.*' ] )
strict_starts_no_opt_attributes = \
text_extraction.extract_annotations_xml( ingest_file ,
offset_mapping = {} ,
annotation_path = \
'./custom:Problems' ,
tag_name = 'Problem' ,
namespaces = namespaces ,
begin_attribute = 'begin' ,
end_attribute = 'end' ,
optional_attributes = [] )
strict_starts_with_opt_attributes = \
text_extraction.extract_annotations_xml( ingest_file ,
offset_mapping = {} ,
annotation_path = \
'./custom:Problems' ,
tag_name = 'Problem' ,
namespaces = namespaces ,
begin_attribute = 'begin' ,
end_attribute = 'end' ,
optional_attributes = \
patterns[ 0 ][ 'optional_attributes' ] )
expected_output_no_opt_attributes = \
{ '181' : [ { 'type': 'Problem' ,
'begin_pos': '181' ,
'end_pos': '188' ,
'raw_text': None } ] ,
'218' : [ { 'type': 'Problem' ,
'begin_pos': '218' ,
'end_pos': '224' ,
'raw_text': None } ]
}
expected_output_with_opt_attributes = \
{ '181' : [ { 'type': 'Problem' ,
'begin_pos': '181' ,
'end_pos': '188' ,
'raw_text': None ,
'conditional' : 'true' ,
'generic' : 'false' ,
'historical' : 'false' ,
'negated' : 'false' ,
'not_patient' : 'true' ,
'uncertain' : 'false' } ] ,
'218' : [ { 'type': 'Problem' ,
'begin_pos': '218' ,
'end_pos': '224' ,
'raw_text': None ,
'conditional' : 'false' ,
'generic' : 'false' ,
'historical' : 'true' ,
'negated' : 'false' ,
'not_patient' : 'false' ,
'uncertain' : 'true' } ]
}
assert strict_starts_no_opt_attributes == \
expected_output_no_opt_attributes
assert strict_starts_with_opt_attributes == \
expected_output_with_opt_attributes
assert strict_starts_no_opt_attributes != \
expected_output_with_opt_attributes
assert strict_starts_with_opt_attributes != \
expected_output_no_opt_attributes
