danich1
commented
2 years ago Greetings. Before I get down into the weeds of this problem, you might want to directly download the xml files here. This might save you time and effort if your main goal is to have converted xml files. Otherwise, it seems to be that the issue is the downloaded file may be corrupted.
Hello, I followed the instructions in the readme, in order to run pubtator locally. But when I have to execute the last command
python execute.py --config config_files/pubtator_central_config.jsonafter the repository is downloaded, I get an error that may be related to the fact that the extraction of the downloaded file doesn't go well. I append the error message:Article that broke: 35401401 228155it [3:57:28, 19.85it/s]Traceback (most recent call last): File "execute.py", line 43, in <module> convert_pubtator( File "/home/gabbo/Tesi/pubtator/scripts/pubtator_to_xml.py", line 181, in convert_pubtator for article in tqdm.tqdm(article_generator): File "/home/gabbo/anaconda3/envs/pubtator/lib/python3.8/site-packages/tqdm/_tqdm.py", line 833, in __iter__ for obj in iterable: File "/home/gabbo/Tesi/pubtator/scripts/pubtator_to_xml.py", line 146, in read_bioconcepts2pubtator_offsets g = list(g) File "/home/gabbo/Tesi/pubtator/scripts/pubtator_to_xml.py", line 141, in <genexpr> lines = (line.rstrip() for line in f) File "/home/gabbo/anaconda3/envs/pubtator/lib/python3.8/gzip.py", line 305, in read1 return self._buffer.read1(size) File "/home/gabbo/anaconda3/envs/pubtator/lib/python3.8/_compression.py", line 68, in readinto data = self.read(len(byte_view)) File "/home/gabbo/anaconda3/envs/pubtator/lib/python3.8/gzip.py", line 487, in read uncompress = self._decompressor.decompress(buf, size) zlib.error: Error -3 while decompressing data: invalid code lengths setCould you please check this problem, and let me know if a fresh install works?
Thank you.