removed not used code from get_uid, added get_uid tests, #436

ropensci · Jun 26, 2015 · 62321ed · 62321ed
1 parent 63055e5
commit 62321ed
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Showing 2 changed files with 43 additions and 4 deletions.
diff --git a/R/get_uid.R b/R/get_uid.R
@@ -147,7 +147,6 @@ get_uid <- function(sciname, ask = TRUE, verbose = TRUE, rows = NA, modifier = N
     if (!is.null(modifier)) sciname <- paste0(sciname, sprintf("[%s]", modifier))
     url <- paste("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=",
                  sciname, sep = "")
-    if (!is.null(division_query)) url <- paste0(url, sprintf(" AND %s[Division]", division_query))
     if (!is.null(rank_query)) url <- paste0(url, sprintf(" AND %s[Rank]", rank_query))
     url <- URLencode(url)
     errors_to_catch <- c("Could not resolve host: eutils.ncbi.nlm.nih.gov")

diff --git a/tests/testthat/test-get_uid.R b/tests/testthat/test-get_uid.R
@@ -2,16 +2,56 @@
 context("get_uid")
 
 test_that("get_uid returns the correct value", {
-	expect_that(is.na(get_uid(c("Chironomus riparius", "aaa"), verbose=FALSE)[2]), 
+	expect_that(is.na(get_uid(c("Chironomus riparius", "aaa"), verbose=FALSE)[2]),
               is_true())
 })
 
 test_that("get_uid returns the correct class", {
-	expect_that(get_uid(c("Chironomus riparius", "Chaetopteryx"), verbose=FALSE), 
+	expect_that(get_uid(c("Chironomus riparius", "Chaetopteryx"), verbose=FALSE),
               is_a("uid"))
 })
 
 test_that("get_uid accepts ask-argument", {
-  expect_that(is.na(get_uid('Dugesia', ask = FALSE, verbose=FALSE)), 
+  expect_that(is.na(get_uid('Dugesia', ask = FALSE, verbose=FALSE)),
               is_true())
 })
+
+test_that("get_uid query modifiers work", {
+  ### w/ modifiers to the name
+  mod1 <- get_uid(sciname = "Aratinga", verbose=FALSE)
+  mod2 <- get_uid(sciname = "Aratinga", modifier = "Organism", rows = 1, verbose=FALSE)
+
+  expect_is(mod1, "uid")
+  expect_is(mod2, "uid")
+  expect_equal(mod1[[1]], "12945")
+  expect_equal(mod2[[1]], "867384")
+
+  ### w/ rank query
+  rq1 <- get_uid(sciname = "Pinus", rank_query = "genus", verbose=FALSE)
+  rq2 <- get_uid(sciname = "Pinus", rank_query = "subgenus", verbose=FALSE)
+
+  expect_is(rq1, "uid")
+  expect_is(rq2, "uid")
+  expect_equal(rq1[[1]], "3337")
+  expect_equal(rq2[[1]], "139271")
+})
+
+test_that("get_uid filtering works", {
+  ### w/ division
+  df1 <- get_uid(sciname = "Echinacea", division_filter = "eudicots", verbose=FALSE)
+  df2 <- get_uid(sciname = "Echinacea", division_filter = "sea urchins", verbose=FALSE)
+
+  expect_is(df1, "uid")
+  expect_is(df2, "uid")
+  expect_equal(df1[[1]], "53747")
+  expect_equal(df2[[1]], "7674")
+
+  ## Rank example
+  rf1 <- get_uid(sciname = "Pinus", rank_filter = "genus", rows = 2, verbose=FALSE)
+  rf2 <- get_uid(sciname = "Pinus", rank_filter = "subgenus", verbose=FALSE)
+
+  expect_is(rf1, "uid")
+  expect_is(rf2, "uid")
+  expect_equal(rf1[[1]], "3337")
+  expect_equal(rf2[[1]], "139271")
+})