Nothing
# LIBS
library(testthat)
# VARS
nrcrds <- 10 # how many fake records to test on?
wd <- getwd()
data_d <- testdatadir_get()
# DATA
records <- readRDS(file = file.path(data_d, 'records.RData'))
# SETUP
cleanup()
setup()
df <- gb_df_generate(records = sample(records, size = nrcrds))
ids <- as.character(df[['accession']])
gb_sql_add(df = df)
# RUNNING
context('Testing \'rentrez-wrappers\'')
test_that('entrez_fetch() works', {
# TODO, what if an ID that is not in the local db is given?
fasta_res <- entrez_fetch(db = 'nucleotide', id = sample(ids, 2),
rettype = 'fasta')
gb_res <- entrez_fetch(db = 'nucleotide', id = sample(ids, 2),
rettype = 'gb')
# xml is not supported, rentrez will be called
res <- with_mock(
`rentrez:::entrez_fetch` = function(...) TRUE,
entrez_fetch(db = 'nucleotide', id = sample(ids, 2),
rettype = 'gb', retmode = 'xml')
)
expect_true(res)
})
cleanup()
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