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pcantalupo avatar pcantalupo commented on August 28, 2024

After code fix, the exception that was occurring is revealed (thrown by Bio::DB::EUtilities)

------------- EXCEPTION -------------
MSG: NCBI esummary fatal error: Invalid uid LXPA01121130.1 at position=0
STACK Bio::Tools::EUtilities::parse_data bioperl/Bio-EUtilities/lib/Bio/Tools/EUtilities.pm:327
STACK Bio::Tools::EUtilities::next_DocSum bioperl/Bio-EUtilities/lib/Bio/Tools/EUtilities.pm:909
STACK Bio::DB::EUtilities::next_DocSum bioperl/Bio-EUtilities/lib/Bio/DB/EUtilities.pm:856

The issue was due to an endless do loop since an exception always occurred therefore $@ was always true. I added a limit on the maximum number of eutils requests to fix this issue.

Here is the HTTP response from NCBI if you manually use the eutils HTTP query
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nucleotide&id=LXPA01121130.1&email=pcantalupo%40gmail.com&retmode=text

<eSummaryResult>
<ERROR>Invalid uid LXPA01121130.1 at position=0</ERROR>
</eSummaryResult>

from annotater.

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