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fix betydb tests #123

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merged 3 commits into from
Aug 19, 2020
Merged

fix betydb tests #123

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b0bb316
Merge pull request #6 from ropensci/master
dlebauer Aug 18, 2020
6ca42cb
Update betydb.R
dlebauer Aug 18, 2020
1fd8574
update tests
dlebauer Aug 18, 2020
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2 changes: 1 addition & 1 deletion R/betydb.R
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Original file line number Diff line number Diff line change
Expand Up @@ -365,7 +365,7 @@ betydb_experiment <- function(id, api_version = NULL, betyurl = NULL, fmt = "jso

betydb_auth <- function(user,pwd,key){
if (is.null(key) && is.null(user)) {
key <- getOption("betydb_key", '9999999999999999999999999999999999999999')
key <- getOption("betydb_key", 'eI6TMmBl3IAb7v4ToWYzR0nZYY07shLiCikvT6Lv')
}
if (!is.null(key)) {
auth <- list(key = key)
Expand Down
34 changes: 8 additions & 26 deletions tests/testthat/test-betydb.R
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Expand Up @@ -6,29 +6,13 @@ test_that("Broken Function", {
expect_error(betydb_traits(genus = "Miscanthus", author = "Arundale", trait = "yield"))
})

test_that("BETYdb v0 API works", {
test_that("BETYdb v1 API works", {
skip_on_cran()
check_betydb()

## gh-18
betyurl <- "https://www.betydb.org/"
priors_url <- makeurl("priors", fmt = "json", betyurl = betyurl)
expect_equal(priors_url, paste0(betyurl, "priors.json"))

# Priors is a small table
get.out <- GET(paste0(priors_url, "/?key=eI6TMmBl3IAb7v4ToWYzR0nZYY07shLiCikvT6Lv"))
expect_is(get.out, "response")
expect_match(httr::headers(get.out)$status, "OK")
expect_match(get.out$url, betyurl)
})

test_that("BETYdb beta API works", {
skip_on_cran()
check_betydb()

betyurl <- "https://www.betydb.org/"
priors_url <- makeurl("priors", fmt = "json", betyurl = betyurl, api_version = "beta")
expect_equal(priors_url, paste0(betyurl, "api/beta/priors.json"))
priors_url <- makeurl("priors", fmt = "json", betyurl = betyurl, api_version = "v1")
expect_equal(priors_url, paste0(betyurl, "api/v1/priors.json"))

get.out <- GET(paste0(priors_url, "/?key=eI6TMmBl3IAb7v4ToWYzR0nZYY07shLiCikvT6Lv")) # Priors is a small table
expect_is(get.out, "response")
Expand All @@ -42,15 +26,15 @@ test_that("table to property name matching works", {

getprop <- function(name){
txt <- betydb_http(
makeurl(name, fmt = "json", betyurl = "https://www.betydb.org/", api_version = "beta"),
makeurl(name, fmt = "json", betyurl = "https://www.betydb.org/", api_version = "v1"),
args = list(limit = 1),
key = NULL,
user = NULL,
pwd = NULL)
names(jsonlite::fromJSON(txt, simplifyVector = TRUE, flatten = FALSE)$data)[[1]]
}
tablenames <- c("search", "species", "entities", "citations", "pfts")
expected_propnames <- sapply(tablenames, makepropname, api_version = "beta")
expected_propnames <- sapply(tablenames, makepropname, api_version = "v1")
got_propnames <- sapply(tablenames, getprop)

expect_equal(got_propnames, expected_propnames)
Expand All @@ -77,10 +61,8 @@ test_that("Credentials work", {

prevkey <- options(betydb_key = "NOTVALID")
on.exit(options(prevkey))
# FIXME - should use v0 API for symmetry w/ other calls,
# but v0 skips auth for search table
options(betydb_key = 'NOT A KEY')
expect_error(betydb_search("Acer rubrum", api_version = "beta"), "Unauthorized",
expect_error(betydb_search("Acer rubrum", api_version = "v1"), "Unauthorized",
class = "error")
options(betydb_key = "eI6TMmBl3IAb7v4ToWYzR0nZYY07shLiCikvT6Lv")
optkey <- betydb_search('Acer rubrum')
Expand All @@ -104,7 +86,7 @@ test_that("URL & version options work", {
betydb_api_version = "v0")
opt1 <- betydb_query(author = "Arundale", table = "citations")

options(betydb_url = "http://example.com/", betydb_api_version = "beta")
options(betydb_url = "http://example.com/", betydb_api_version = "v1")
expect_error(betydb_query(author = "Arundale", table = "citations"),
"Not Found", class = "error")
opt2 <- betydb_query(author = "Arundale", table = "citations",
Expand Down Expand Up @@ -138,7 +120,7 @@ test_that("paging works with betydb query and search functions",{
on.exit(reset_opts(opts))
options(
betydb_url = "https://www.betydb.org/",
betydb_api_version = "beta",
betydb_api_version = "v1",
betydb_key = "eI6TMmBl3IAb7v4ToWYzR0nZYY07shLiCikvT6Lv",
per_call_limit = 10, # check paging without a 5000-item request
warn=-1 ## suppress warnings that we did not get all data
Expand Down