Parsers cannot read the xml file. about pubmed_parser HOT 3 CLOSED

Hi @robear22890, thanks for the report and sorry for the late reply! So, I seems like the problem is from reading XML file (etree.from_string(path)). Pubmed parser uses these snippet to read XML file. Can you check real quick if lxml works to read example file for you or the file that you have a problem with?

From the error, it seems like you were using the wrong function to parse MEDLINE XML. For the MEDLINE one, you have to use parse_medline_xml function instead of parse_pubmed_xml. parse_pubmed_xml is actually for Pubmed Open-Access subset XML files. Let me know if this solves the problem.

from pubmed_parser.

@robear22890 @titipata It seems that the problem is that it cannot find the file? As @titipata mentions, pubmed_parser tries to read the given string as if it were a file path and if that fails it tries to read it as a XML string. So it first fails to read the file, and then it tries to read it as an XML. Can you please check that the file exists at that location?

from pubmed_parser.

I am closing this for now

from pubmed_parser.