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Use web history for large NCBI queries to enable downloading of >300 samples #84

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zachary-foster opened this issue Jul 17, 2024 · 1 comment

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@zachary-foster
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Currently, the use of rentrez::entrez_search requires retmax = 300 or we get this error:

Error in entrez_check(response) : 
  HTTP failure 414, the request is too large. For large requests, try using web history as described in the rentrez tutorial

Need to either add a way to loop rentrez::entrez_search or use seb history.

Should also add a global parameter to limit the maximum number of genomes/reads to download.

zachary-foster added a commit to grunwaldlab/pathogensurveillance that referenced this issue Jul 17, 2024
@zachary-foster
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done

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