def process(in_file, in_list, out_file, log_file, tika_server_url,
corenlp_server_url, ner_model, gazette_file, relation_types,
jsre_root, jsre_models, jsre_tmp_dir, ads_url, ads_token):
# Log input parameters
logger = LogUtil(log_file)
logger.info('Input parameters')
logger.info('in_file: %s' % in_file)
logger.info('in_list: %s' % in_list)
logger.info('out_file: %s' % out_file)
logger.info('tika_server_url: %s' % tika_server_url)
logger.info('corenlp_server_url: %s' % corenlp_server_url)
logger.info('ner_model: %s' % os.path.abspath(ner_model))
logger.info('gazette_file: %s' % gazette_file)
logger.info('relation_types: %s' % json.dumps(relation_types))
logger.info('jsre_root: %s' % os.path.abspath(jsre_root))
logger.info('jsre_models: %s' % json.dumps(jsre_models))
logger.info('jsre_tmp_dir: %s' % os.path.abspath(jsre_tmp_dir))
logger.info('ads_url: %s' % ads_url)
logger.info('ads_token: %s' % ads_token)
if in_file and in_list:
print('[ERROR] in_file and in_list cannot be provided simultaneously')
sys.exit(1)
if len(relation_types) != len(jsre_models):
print(
'[ERROR] There should be a one-to-one mapping for relation types '
'and jSRE models.')
sys.exit(1)
ads_parser = AdsParser(ads_token, ads_url, tika_server_url)
jsre_parser = JsreParser(corenlp_server_url, ner_model, gazette_file,
relation_types, jsre_root, jsre_models,
jsre_tmp_dir)
if in_file:
files = [in_file]
else:
files = read_lines(in_list)
out_f = open(out_file, 'wb', 1)
for f in tqdm(files):
try:
ads_dict = ads_parser.parse(f)
jsre_dict = jsre_parser.parse(ads_dict['content'])
ads_dict['metadata']['ner'] = jsre_dict['ner']
ads_dict['metadata']['rel'] = jsre_dict['relation']
ads_dict['metadata']['sentences'] = jsre_dict['sentences']
ads_dict['metadata']['X-Parsed-By'].append(
jsre_dict['X-Parsed-By'])
out_f.write(json.dumps(ads_dict))
out_f.write('\n')
except Exception as e:
logger.info('JSRE parser failed: %s' % os.path.abspath(f))
logger.error(e)
out_f.close()
def process(in_file, in_list, out_file, log_file, tika_server_url,
corenlp_server_url, ner_model, gazette_file, relation_type,
jsre_root, jsre_model, jsre_tmp_dir, ads_url, ads_token):
# Log input parameters
logger = LogUtil('jgr-parser', log_file)
logger.info('Input parameters')
logger.info('in_file: %s' % in_file)
logger.info('in_list: %s' % in_list)
logger.info('out_file: %s' % out_file)
logger.info('tika_server_url: %s' % tika_server_url)
logger.info('corenlp_server_url: %s' % corenlp_server_url)
logger.info('ner_model: %s' % os.path.abspath(ner_model))
logger.info('gazette_file: %s' % gazette_file)
logger.info('relation_type: %s' % relation_type)
logger.info('jsre_root: %s' % os.path.abspath(jsre_root))
logger.info('jsre_model: %s' % os.path.abspath(jsre_model))
logger.info('jsre_tmp_dir: %s' % os.path.abspath(jsre_tmp_dir))
logger.info('ads_url: %s' % ads_url)
logger.info('ads_token: %s' % ads_token)
if in_file and in_list:
print('[ERROR] in_file and in_list cannot be provided simultaneously')
sys.exit(1)
ads_parser = AdsParser(ads_token, ads_url, tika_server_url)
jgr_parser = JgrParser()
jsre_parser = JsreParser(corenlp_server_url, ner_model, gazette_file,
relation_type, jsre_root, jsre_model, jsre_tmp_dir)
if in_file:
files = [in_file]
else:
files = read_lines(in_list)
out_f = open(out_file, 'wb', 1)
for f in tqdm(files):
try:
ads_dict = ads_parser.parse(f)
journal_dict = jgr_parser.parse(ads_dict['content'],
ads_dict['metadata'])
jsre_dict = jsre_parser.parse(journal_dict['cleaned_content'])
ads_dict['content_ann_s'] = journal_dict['cleaned_content']
ads_dict['references'] = journal_dict['references']
ads_dict['metadata']['ner'] = jsre_dict['ner']
ads_dict['metadata']['rel'] = jsre_dict['relation']
ads_dict['metadata']['sentences'] = jsre_dict['sentences']
ads_dict['metadata']['X-Parsed-By'] = jsre_dict['X-Parsed-By']
out_f.write(json.dumps(ads_dict))
out_f.write('\n')
except Exception as e:
logger.info('JGR parser failed: %s' % os.path.abspath(f))
logger.error(e)
out_f.close()
def process(in_file, in_list, out_file, log_file, tika_server_url,
corenlp_server_url, ner_model, gazette_file, ads_url, ads_token):
# Log input parameters
logger = LogUtil('corenlp-parser', log_file)
logger.info('Input parameters')
logger.info('in_file: %s' % in_file)
logger.info('in_list: %s' % in_list)
logger.info('out_file: %s' % out_file)
logger.info('tika_server_url: %s' % tika_server_url)
logger.info('corenlp_server_url: %s' % corenlp_server_url)
logger.info('ner_model: %s' % os.path.abspath(ner_model))
logger.info('gazette_file: %s' % gazette_file)
logger.info('ads_url: %s' % ads_url)
logger.info('ads_token: %s' % ads_token)
if in_file and in_list:
print('[ERROR] in_file and in_list cannot be provided simultaneously')
sys.exit(1)
ads_parser = AdsParser(ads_token, ads_url, tika_server_url)
corenlp_parser = CoreNLPParser(corenlp_server_url, ner_model, gazette_file)
if in_file:
files = [in_file]
else:
files = read_lines(in_list)
out_f = open(out_file, 'wb', 1)
for f in tqdm(files):
try:
ads_dict = ads_parser.parse(f)
corenlp_dict = corenlp_parser.parse(ads_dict['content'])
ads_dict['metadata']['ner'] = corenlp_dict['ner']
ads_dict['metadata']['X-Parsed-By'].append(
corenlp_dict['X-Parsed-By'])
ads_dict['metadata']['sentences'] = corenlp_dict['sentences']
out_f.write(json.dumps(ads_dict))
out_f.write('\n')
except Exception as e:
logger.info('CoreNLP parser failed: %s' % os.path.abspath(f))
logger.error(e)
out_f.close()
def process(in_file, in_list, out_file, log_file, tika_server_url, ads_url,
ads_token, corenlp_server_url, ner_model, containee_model_file,
container_model_file, entity_linking_method, gpu_id, batch_size):
# Log input parameters
logger = logging.getLogger(
) # @Stevem: Please change the following logging code with your Logger
logger.info('Input parameters')
logger.info('in_file: %s' % in_file)
logger.info('in_list: %s' % in_list)
logger.info('out_file: %s' % out_file)
logger.info('log_file: %s' % log_file)
logger.info('tika_server_url: %s' % tika_server_url)
logger.info('ads_url: %s' % ads_url)
logger.info('ads_token: %s' % ads_token)
logger.info('corenlp_server_url: %s' % corenlp_server_url)
logger.info('ner_model: %s' % os.path.abspath(ner_model))
logger.info('container_model_file: %s' %
os.path.abspath(container_model_file))
logger.info('containee_model_file: %s' %
os.path.abspath(containee_model_file))
logger.info('entity_linking_method: %s' % entity_linking_method)
logger.info('gpu_id: %s' % str(gpu_id))
if in_file and in_list:
raise NameError(
'[ERROR] in_file and in_list cannot be provided simultaneously')
ads_parser = AdsParser(ads_token, ads_url, tika_server_url)
unary_parser = UnaryParser(corenlp_server_url,
ner_model,
containee_model_file,
container_model_file,
gpu_id=gpu_id)
if in_file:
files = [in_file]
else:
files = read_lines(in_list)
out_f = open(out_file, 'wb', 1)
for f in tqdm(files):
try:
ads_dict = ads_parser.parse(f)
unary_dict = unary_parser.parse(
ads_dict['content'],
batch_size=batch_size,
entity_linking_method=entity_linking_method)
ads_dict['metadata']['ner'] = unary_dict['ner']
ads_dict['metadata']['rel'] = unary_dict['relation']
ads_dict['metadata']['sentences'] = unary_dict['sentences']
ads_dict['metadata']['X-Parsed-By'].append(
unary_dict['X-Parsed-By'])
out_f.write(json.dumps(ads_dict))
out_f.write('\n')
except Exception as e:
logger.info('Unary parser failed: %s' % os.path.abspath(f))
logger.error(e)
out_f.close()
def process(in_file, in_list, out_file, log_file, tika_server_url,
corenlp_server_url, ner_model, gazette_file, relation_types,
jsre_root, jsre_models, jsre_tmp_dir, ads_url, ads_token):
# Log input parameters
logger = LogUtil(log_file)
logger.info('Input parameters')
logger.info('in_file: %s' % in_file)
logger.info('in_list: %s' % in_list)
logger.info('out_file: %s' % out_file)
logger.info('tika_server_url: %s' % tika_server_url)
logger.info('corenlp_server_url: %s' % corenlp_server_url)
logger.info('ner_model: %s' % os.path.abspath(ner_model))
logger.info('gazette_file: %s' % gazette_file)
logger.info('relation_types: %s' % json.dumps(relation_types))
logger.info('jsre_root: %s' % os.path.abspath(jsre_root))
logger.info('jsre_model: %s' % json.dumps(jsre_models))
logger.info('jsre_tmp_dir: %s' % os.path.abspath(jsre_tmp_dir))
logger.info('ads_url: %s' % ads_url)
logger.info('ads_token: %s' % ads_token)
if in_file and in_list:
print('[ERROR] in_file and in_list cannot be provided simultaneously')
sys.exit(1)
ads_parser = AdsParser(ads_token, ads_url, tika_server_url)
paper_parser = PaperParser()
jsre_parser = JsreParser(corenlp_server_url, ner_model, gazette_file,
relation_types, jsre_root, jsre_models,
jsre_tmp_dir)
if in_file:
files = [in_file]
else:
files = read_lines(in_list)
out_f = open(out_file, 'wb', 1)
for f in tqdm(files):
logger.info('Processing %s' % os.path.basename(f))
try:
ads_dict = ads_parser.parse(f)
if 'grobid:header_Title' in ads_dict['metadata'].keys():
logger.info('Document title: %s' %
ads_dict['metadata']['grobid:header_Title'])
paper_dict = paper_parser.parse(ads_dict['content'],
ads_dict['metadata'])
jsre_dict = jsre_parser.parse(paper_dict['cleaned_content'])
ads_dict['content_ann_s'] = paper_dict['cleaned_content']
ads_dict['metadata']['ner'] = jsre_dict['ner']
ads_dict['metadata']['rel'] = jsre_dict['relation']
ads_dict['metadata']['sentences'] = jsre_dict['sentences']
ads_dict['metadata']['X-Parsed-By'] = jsre_dict['X-Parsed-By']
out_f.write(json.dumps(ads_dict))
out_f.write('\n')
except Exception as e:
logger.info('Paper parser failed: %s' % os.path.abspath(f))
logger.error(e)
out_f.close()
def process(in_file, in_list, out_file, log_file, tika_server_url,
corenlp_server_url, ner_model, gazette_file, relation_types,
jsre_root, jsre_models, jsre_tmp_dir, containee_model_file,
container_model_file, entity_linking_method, gpu_id, batch_size,
ads_url, ads_token):
# Log input parameters
logger = LogUtil(log_file)
logger.info('Input parameters')
logger.info('in_file: %s' % in_file)
logger.info('in_list: %s' % in_list)
logger.info('out_file: %s' % out_file)
logger.info('tika_server_url: %s' % tika_server_url)
logger.info('corenlp_server_url: %s' % corenlp_server_url)
logger.info('ner_model: %s' % os.path.abspath(ner_model))
logger.info('gazette_file: %s' % gazette_file)
logger.info('ads_url: %s' % ads_url)
logger.info('ads_token: %s' % ads_token)
if in_file and in_list:
logger.info('[ERROR] in_file and in_list cannot be provided '
'simultaneously')
sys.exit(1)
if len(relation_types) != len(jsre_models):
print('[ERROR] There should be a one-to-one mapping for relation types '
'and jSRE models.')
sys.exit(1)
ads_parser = AdsParser(ads_token, ads_url, tika_server_url)
lpsc_parser = LpscParser()
# Note: this is temporary solution as it requires users to carefully provide
# inputs to the script. A better solution would be restrict users to provide
# inputs that are mutual exclusive (e.g., if jsre_model is provided, then
# unary parser's options should be disallowed).
# Steven Lu, September 2, 2021
jsre_parser = None
unary_parser = None
if jsre_models:
logger.info('relation_types: %s' % json.dumps(relation_types))
logger.info('jsre_root: %s' % os.path.abspath(jsre_root))
logger.info('jsre_models: %s' % json.dumps(jsre_models))
logger.info('jsre_tmp_dir: %s' % os.path.abspath(jsre_tmp_dir))
jsre_parser = JsreParser(corenlp_server_url, ner_model, gazette_file,
relation_types, jsre_root, jsre_models,
jsre_tmp_dir)
elif container_model_file and containee_model_file and entity_linking_method:
logger.info('container_model_file: %s' %
os.path.abspath(container_model_file))
logger.info('containee_model_file: %s' %
os.path.abspath(containee_model_file))
logger.info('entity_linking_method: %s' % entity_linking_method)
logger.info('gpu_id: %s' % str(gpu_id))
unary_parser = UnaryParser(corenlp_server_url, ner_model, gazette_file,
containee_model_file, container_model_file,
gpu_id=gpu_id)
if in_file:
files = [in_file]
else:
files = read_lines(in_list)
out_f = open(out_file, 'wb', 1)
for f in tqdm(files):
try:
base_name = os.path.basename(f)
logger.info('Processing %s' % base_name)
base_name = base_name.split('.')[0]
year, abs_num = base_name.split('_')
query_dict = {'lpsc_query_strategy': {
'year': year,
'abstract_number': abs_num
}}
ads_dict = ads_parser.parse(f, query_dict)
lpsc_dict = lpsc_parser.parse(ads_dict['content'],
ads_dict['metadata'])
if jsre_parser is not None:
rel_dict = jsre_parser.parse(lpsc_dict['cleaned_content'])
else:
rel_dict = unary_parser.parse(
lpsc_dict['cleaned_content'], batch_size=batch_size,
entity_linking_method=entity_linking_method)
ads_dict['content_ann_s'] = lpsc_dict['cleaned_content']
ads_dict['references'] = lpsc_dict['references']
ads_dict['metadata']['ner'] = rel_dict['ner']
ads_dict['metadata']['rel'] = rel_dict['relation']
ads_dict['metadata']['sentences'] = rel_dict['sentences']
ads_dict['metadata']['X-Parsed-By'] = rel_dict['X-Parsed-By']
out_f.write(json.dumps(ads_dict))
out_f.write('\n')
except Exception as e:
logger.info('LPSC parser failed: %s' % os.path.abspath(f))
logger.error(e)
out_f.close()