Merge branch 'master' into allow-redirects

.github/workflows/r-package.yml

@@ -4,9 +4,10 @@ on: push
 
 jobs:
   solvebio-R:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     env:
-      SOLVEBIO_API_KEY: ${{ secrets.SOLVEBIO_API_KEY }}
+      SOLVEBIO_API_HOST: ${{ secrets.QUARTZBIO_API_HOST }}
+      SOLVEBIO_API_KEY: ${{ secrets.QUARTZBIO_API_KEY }}
     steps:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v1

DESCRIPTION

@@ -38,7 +38,7 @@ Collate:
     utils.R
     vault.R
     zzz.R
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Suggests:
     testthat,

tests/testthat/test_env.R

@@ -7,12 +7,16 @@ bad_env <- solvebio::createEnv("bad")
 # NOTE: good_env only works if assert_api_key()
 good_env <- solvebio::createEnv(solvebio:::.solveEnv$token)
 
+is_valid_email <- function(email) {
+  grepl("\\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\\.[A-Z]{2,}\\b", email, ignore.case = TRUE)
+}
+
 
 test_that("createEnv properly sets defaults", {
               env <- solvebio::createEnv("token")
               expect_equal(env$token, "token")
               expect_equal(env$token_type, "Token")
-              expect_equal(env$host, "https://api.solvebio.com")
+              expect_type(env$host, "character")
 })
 
 test_that("A default env is created", {
@@ -27,14 +31,14 @@ test_that("Simple functions work with global and local envs", {
 
               # Global env should work
               user <- User.retrieve()
-              expect_equal(user$email, "[email protected]")
+              expect_true(is_valid_email(user$email))
 
               # Local env should error
               expect_error(User.retrieve(env=bad_env), ".*401.*")
 
               # Local env with global's token should work
               user <- User.retrieve(env=good_env)
-              expect_equal(user$email, "[email protected]")
+              expect_true(is_valid_email(user$email))
 })
 
 test_that("Functions with ellipsis work with global and local envs", {
@@ -84,7 +88,7 @@ test_that("do.call works with env argument", {
 
               # Simple functions
               user <- do.call(User.retrieve, c(good_env))
-              expect_equal(user$email, "[email protected]")
+              expect_true(is_valid_email(user$email))
               expect_error(do.call(User.retrieve, c(bad_env)), ".*401.*")
 
               # Functions with ellipsis

tests/testthat/test_query.R

@@ -6,16 +6,13 @@ source("./helpers.R", local=T)
 # NOTE: good_env only works if assert_api_key()
 env <- solvebio::createEnv(solvebio:::.solveEnv$token)
 
-TEST_DATASET_FULL_PATH_2 <- 'solvebio:public:/ClinVar/5.1.0-20200720/Variants-GRCH38'
+TEST_DATASET_FULL_PATH_2 <- 'quartzbio:public:/ClinVar/5.3.0-20231007/Variants-GRCH38'
 
 test_that("Query the dataset and check that titles are colnames in df", {
               assert_api_key()
 
-              user <- User.retrieve(env=env)
-              expect_equal(user$email, "[email protected]")
-
               ds <- Dataset.get_by_full_path(TEST_DATASET_FULL_PATH_2)
               query <- Dataset.query(ds$id, fields=list("variant", "_id", "disease", "allele"), use_field_titles=TRUE)
               expect_true('_id' %in% colnames(query))
 
-})
+})