Nothing
# Test efetch() -----------------------------------------------------------
context("Testing 'efetch()'")
if (getOption('reutils.test.remote')) {
test_that("Fetch PMIDs 17284678 and 9997 as text abstracts", {
a <- efetch(uid = c(17284678, 9997), db = 'pubmed', rettype = 'abstract')
expect_equal(retmode(a), "text")
expect_equal(rettype(a), "abstract")
## Content
expect_is(content(a), 'character')
expect_is(content(a, "text"), 'character')
expect_error(content(a, 'xml'), "Cannot return data of retmode.+")
expect_error(content(a, 'json'), "Cannot return data of retmode.+")
expect_is(content(a, 'parsed'), 'character')
expect_is(content(a, 'textConnection'), 'textConnection')
})
test_that("Fetch PMIDs 17284678 and 9997 as XML", {
a <- efetch(c(17284678, 9997), 'pubmed', retmode = 'xml')
expect_equal(retmode(a), "xml")
expect_equal(rettype(a), "")
## Content
expect_is(content(a), 'XMLInternalDocument')
expect_is(content(a, "text"), 'character')
expect_is(content(a, 'xml'), "XMLInternalDocument")
expect_error(content(a, 'json'), "Cannot return data of retmode.+")
expect_is(content(a, 'parsed'), 'XMLInternalDocument')
expect_error(content(a, 'textConnection'), "Cannot return data of retmode.+")
})
test_that("Fetch 100 bases of the minus strand of GI 21614549", {
a <- efetch('21614549', 'nuccore', strand = 1, seqstart = 1, seqstop = 100,
rettype = "fasta", retmode = "text")
expect_equal(retmode(a), "text")
expect_equal(rettype(a), "fasta")
expect_equal(nchar(paste0(strsplit(content(a), '\n')[[1]][-1], collapse = "")), 100)
})
test_that("efetch works with UIDs provided as character or numeric vectors", {
a <- efetch(c(28800982, 28628843), "protein", "fasta")
## sometimes NCBI returns an empty TSeqSet for whatever reason. This completely
## breaks the test so we better check for that scenario
if (!all(is.na(a$xmlName("//TSeqSet/*")))) {
expect_equal(a$xmlName("//TSeqSet/*"), c("TSeq", "TSeq"))
}
})
test_that("efetch works with an esearch object as input", {
x <- esearch("erythroid associated factor AND Homo sapiens", 'protein', retmax = 2)
a <- efetch(x, rettype = "fasta")
if (!all(is.na(a$xmlValue("//TSeq_taxid")))) {
expect_equal(a$xmlValue("//TSeq_taxid"), c("9606", "9606"))
}
})
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.