rentrez
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Using web history instead of ids returns more results than expected
When I run entrez_search()
with use_history
and retmax = 5
, the function will respect this and return 5 UIDs:
biosample_uid <- entrez_search(db = "biosample", term = "Microthrix parvicella", use_history = TRUE, retmax = 5)
length(biosample_uid$ids)
5
When I convert these to assembly UID without using web history, the entrez_link()
will return 5 UIDs, as expected:
assembly_uid <- entrez_link(dbfrom = "biosample", id = biosample_uid$ids, db = "assembly")
length(assembly_uid$links$biosample_assembly)
5
However, when I use the web history, the function will return more than 5 UIDs:
assembly_uid <- entrez_link(dbfrom = "biosample", web_history = biosample_uid$web_history, db = "assembly")
length(assembly_uid$links$biosample_assembly)
14
Even if I set retmax
:
assembly_uid <- entrez_link(dbfrom = "biosample", web_history = biosample_uid$web_history, db = "assembly", retmax = 5)
length(assembly_uid$links$biosample_assembly)
14
It seems this is not an entrez_link()
thing, it also occurs e.g. with entrez_fetch()
:
meta <- entrez_fetch(db = "biosample", web_history = biosample_uid$web_history, rettype = "full", retmode = "xml")
xmllist <- xml2::as_list(xml2::read_xml(meta))[[1]]
length(xmllist)
16
Again, ids instead of web history work fine:
meta <- entrez_fetch(db = "biosample", id = biosample_uid$ids, rettype = "full", retmode = "xml")
xmllist <- xml2::as_list(xml2::read_xml(meta))[[1]]
length(xmllist)
5
Any idea what is going on here? Many thanks.