I am trying to use Entrez to search and parse publication records from PubMed. The parse function used to work until recently, but a few days ago it started failing. I started getting the following error:
File "/venv/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 296, in parse raise ValueError("The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse") ValueError: The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse
Looking at the source code (http://biopython.org/DIST/docs/api/Bio.Entrez-pysrc.html) and trying to follow the listed example, gives the same error.
from Bio import Entrez Entrez.email = "Your.Name.Here@example.org" handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml") records = Entrez.parse(handle) for record in records: print(record['MedlineCitation']['Article']['ArticleTitle']) handle.close()
Does somebody have an idea what might be going wrong here?