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Article ID parsing issue. #1

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iacopy opened this issue Feb 25, 2022 · 0 comments · Fixed by #4
Closed

Article ID parsing issue. #1

iacopy opened this issue Feb 25, 2022 · 0 comments · Fixed by #4
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@iacopy
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iacopy commented Feb 25, 2022 •
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See gijswobben#22

Describe the bug
A report the first report of this

While iterating on articles resulting from a PubMed query, I noticed that some article ids have parsing issues.

For instance :
Query : ((Haliaeetus leucocephalus[Title/Abstract])) AND ((prey[Title/Abstract]) OR (diet[Title/Abstract]))

Returns (when printing first 10 results) :
pubmed_id = '22822430\n18959310\n21310968\n21295371\n20439737'
abstract = ('Bald eagles (Haliaeetus leucocephalus) are recovering from severe population declines...

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  • OS: [e.g. Windows / Linux]
  • Version [e.g. Python 3.7.0]

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@iacopy iacopy added the bug Something isn't working label Feb 25, 2022
@iacopy iacopy mentioned this issue Feb 25, 2022
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iacopy added a commit that referenced this issue Feb 25, 2022
@iacopy
Fix parsing of article ID
3fb1a38 
Fix #1

This fix avoids returning also the IDs of cited
papers
(they are within the ReferenceList element of the xml).

Note: this issue was tracked as 22 on the original repository (now archived)

An alternative XPath to be used:
path = ".//PubmedData/ArticleIdList/ArticleId[@idtype='pubmed']"
@iacopy iacopy mentioned this issue Feb 25, 2022
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@iacopy iacopy closed this as completed in #4 Feb 25, 2022
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Fix parsing of article ID iacopy/pymed
Fix parsing of article ID iacopy/pymed
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