XMLSyntaxError

[deakkon]

In [41]: pp.parse_medline_xml('/home/docClass/files/pubmed/pubmed18n1040.xml.gz')
Error: it was not able to read a path, a file-like object, or a string as an XML
File "", line 1
XMLSyntaxError: Start tag expected, '<' not found, line 1, column 1

Source: ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed18n1040.xml.gz

[daniel-acuna]

I don't think parse_medline_xml parses .gz files. You need to uncompress it first.

[deakkon]

Hi,

are you sure?
E.g. pp.parse_medline_xml('pubmed18n0364.xml.gz') (source ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed18n0364.xml.gz)

gives back a list of dicts.

[daniel-acuna]

Can you try uncompress it first? The file works for me

[deakkon]

Sorry, my mistake! The issues was that the file was not properly downloaded (Im performing a batch download and no error was printed out).

Redownloaded it manually and it works directly from the path (skipping uncompressing).

Best,
J.