context("search")
#setup
gsearch <- entrez_global_query("Heliconius")
pubmed_search <- entrez_search(db = "pubmed",
term = "10.1016/j.ympev.2010.07.013[doi]")
json_search <- entrez_search(db="pubmed",
term = "10.1016/j.ympev.2010.07.013[doi]",
retmode='json')
test_that("Global query works",{
#global query
expect_that(gsearch, is_a("numeric"))
expect_that(names(gsearch), is_a("character"))
#now includes 'database error' for some databaes
#these are made NA in entrez_global_query, which seems reasonable
expect_true(sum(gsearch, na.rm=TRUE) > 0 )
})
test_that("Entrez query works",{
#entrez query
expect_that(pubmed_search, is_a("esearch"))
expect_that(pubmed_search$ids, is_identical_to("20674752"))
})
test_that("Entrez query works just as well with xml/json",{
expect_that(json_search, is_a("esearch"))
expect_that(json_search$ids, is_identical_to("20674752"))
expect_equal(names(pubmed_search),names(json_search))
})
test_that("we can print search results", {
expect_output(print(pubmed_search), "Entrez search result with \\d+ hits")
expect_output(print(json_search), "Entrez search result with \\d+ hits")
})
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