def annotate_doc(pdf_file_path, ontologies):
if pdf_file_path.endswith('pdf') or pdf_file_path.endswith('PDF'):
text = textract.process(pdf_file_path, method="pdfminer")
elif pdf_file_path.endswith('html') or pdf_file_path.endswith('htm'):
text = textract.process(pdf_file_path, method="beautifulsoup4")
elif pdf_file_path.endswith('txt'):
with open(pdf_file_path, 'r') as file:
text = file.read()
db = DBConnect()
if text.isspace():
log = {
'file_name': pdf_file_path.encode('utf-8'),
'error': 'Failed PDF to text transformation in annotation process',
'exception': '',
'data': ''
}
db.insert_log(log)
return
ontologies = ",".join(ontologies)
annotations = []
text = unidecode(text.decode('utf8'))
text = ' '.join(text.split())
# post_data = dict(apikey=settings.BIOPORTAL_API_KEY, text=text,
# display_links='true', display_context='false', minimum_match_length='3',
# exclude_numbers='true', longest_only='true', ontologies=ontologies, exclude_synonyms='true')
post_data = dict(apikey=settings.BIOPORTAL_API_KEY, text=text,
display_links='true', display_context='false', minimum_match_length='3',
exclude_numbers='true', longest_only='true', ontologies=ontologies, exclude_synonyms='true')
try:
response = requests.post(settings.ANNOTATOR_URL, post_data)
json_results = json.loads(response.text)
for result in json_results:
for annotation in result['annotations']:
context_begin = annotation['from'] if annotation['from'] - 40 < 1 else annotation['from'] - 40
context_end = annotation['to'] if annotation['to'] + 40 > len(text) else annotation['to'] + 40
record = {
'file_name': pdf_file_path.encode('utf-8'),
'bio_class_id': result['annotatedClass']['@id'],
'bio_ontology_id': result['annotatedClass']['links']['ontology'],
'text': u'' + annotation['text'].encode('utf-8'),
'match_type': annotation['matchType'],
'context': u''+text[context_begin:context_end]
}
annotations.append(record)
db.insert_annotations(annotations)
return
except (ValueError, IndexError, KeyError) as e:
print e
log = {
'file_name': pdf_file_path.encode('utf-8'),
'error': 'Bad response from Bioportal Annotator',
'exception': str(e),
'data': ''
}
db.insert_log(log)
return
