Comments (4)
I don't think parse_medline_xml
parses .gz
files. You need to uncompress it first.
from pubmed_parser.
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.
from pubmed_parser.
Can you try uncompress it first? The file works for me
from pubmed_parser.
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.
from pubmed_parser.
Related Issues (20)
- Upload package on PyPI HOT 3
- Example of processing in dask rather than pyspark HOT 2
- medline_parser has syntax error: `"is not" with a literal` HOT 1
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- All of PubMed XML was updated to follow the MEDLINE XML format.
- PMC OA: tags in the <journal-title> field break parse_pubmed_xml HOT 1
- parse_pubmed_paragraph() function seems to miss some paragraphs sometimes.
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- Error: parse_medline_xml() is unable to parse the file even though the provided path is correct HOT 11
- AttributeError: 'NoneType' object has no attribute 'find' HOT 2
- Table parsing issues with parse_pubmed_table HOT 2
- parse_pubmed_table() and parse_pubmed_references() returning None HOT 1
- Question for extracting text HOT 1
- Question: Abstract with Mesh Tag HOT 3
- question using pp.parese_medline HOT 2
- Question: parsing error first line expecting '<' not found
- parse_pubmed_caption() failing on some papers
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- Bug report - XML citations from website HOT 1
- CALL FOR MAINTAINER/CONTRIBUTOR FOR PUBMED_PARSER HOT 7
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from pubmed_parser.