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Incomplete text (abstract or title) #2

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iacopy opened this issue Feb 25, 2022 · 1 comment
Closed

Incomplete text (abstract or title) #2

iacopy opened this issue Feb 25, 2022 · 1 comment
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@iacopy
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iacopy commented Feb 25, 2022

Describe the bug

See gijswobben#23

While iterating on articles resulting from a PubMed query, I also noticed that the abstract is sometimes incomplete :

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

Returns (when printing first 10 results) :
pubmed_id = '31015971'
abstract = 'Bald eagle ('

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@iacopy iacopy added the bug Something isn't working label Feb 25, 2022
iacopy added a commit that referenced this issue Feb 25, 2022
@iacopy
Fix many incomplete abstract and title issues
8f373ff 
In some cases the title and/or abstract obtained was incomplete
(issue #2) -- 23 in the original pymed repo.

This happens when the text contains html markup tags
(<b>, <i>, <sub>, <sup>, ...).

Example: PMID 31689885
<ArticleTitle>Gamma Irradiated <i>Rhodiola sachalinensis</i> Extract Ameliorates [...]</ArticleTitle>
Before the fix the returned title was just: 'Gamma Irradiated '
<AbstractText>The effect of <i>Rhodiola sachalinensis</i> Boriss extract irradiated [...]</ArticleTitle>
Before the fix the returned abstract was just: 'The effect of '

Fastest solution found: cleanup of frequently used html markup tags like <b>, <i>, <sub>, <sup>.
It seems to fix most of papers correctly, at least for the above mentioned tags.
@iacopy
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iacopy commented Feb 25, 2022

Fixed in PR #5

@iacopy iacopy closed this as completed Feb 25, 2022
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