I get the following error when running main.py. How can I resolve this please ?
"Traceback (most recent call last):
File "C:\Users\SuresMal\Anaconda3\lib\site-packages\IPython\core\interactiveshell.py", line 3331, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 45, in
df = ctakes_concept_extraction(data_dir, ctakes_folder, hard_section_list)
File "C:\Users\SuresMal\Documents\GitHub\clneg\src\concept_extraction.py", line 60, in ctakes_concept_extraction
d = [e for e in extract_cuis(data_dir + 'tmp.xml')]
File "C:\Users\SuresMal\Documents\GitHub\clneg\src\concept_extraction.py", line 26, in extract_cuis
cui_spans = get_cui_spans(xml_filename)
File "C:\Users\SuresMal\Documents\GitHub\clneg\src\concept_extraction.py", line 10, in get_cui_spans
tree = etree.parse(xml_filename)
File "src/lxml/etree.pyx", line 3519, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1839, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1865, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1769, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1163, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 601, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError
File "../data/tmp.xml", line 5
[SECTION-History of Present Illness-START]
^
XMLSyntaxError: Start tag expected, '<' not found, line 5, column 1"
Note:
I'm running on a windows machine
I am running the code for main.py line by line on a jupyter notebook (in the same dir as main.py)
I get the following error when running main.py. How can I resolve this please ?
"Traceback (most recent call last):
File "C:\Users\SuresMal\Anaconda3\lib\site-packages\IPython\core\interactiveshell.py", line 3331, in run_code exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 45, in
df = ctakes_concept_extraction(data_dir, ctakes_folder, hard_section_list)
File "C:\Users\SuresMal\Documents\GitHub\clneg\src\concept_extraction.py", line 60, in ctakes_concept_extraction d = [e for e in extract_cuis(data_dir + 'tmp.xml')]
File "C:\Users\SuresMal\Documents\GitHub\clneg\src\concept_extraction.py", line 26, in extract_cuis cui_spans = get_cui_spans(xml_filename)
File "C:\Users\SuresMal\Documents\GitHub\clneg\src\concept_extraction.py", line 10, in get_cui_spans tree = etree.parse(xml_filename)
File "src/lxml/etree.pyx", line 3519, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1839, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1865, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1769, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1163, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 601, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError
File "../data/tmp.xml", line 5 [SECTION-History of Present Illness-START] ^ XMLSyntaxError: Start tag expected, '<' not found, line 5, column 1"
Note: