From 6ed2c4164b0b2e8addab8085c84fb5f746a607d2 Mon Sep 17 00:00:00 2001
From: Levi Waldron <lwaldron.research@gmail.com>
Date: Sat, 31 Oct 2026 23:55:03 -0400
Subject: [PATCH] Add host argument to BEDbase()

Closes #5

Co-authored-by: Claude Code <noreply@anthropic.com>
---
 R/bedbaser.R                   | 13 ++++++++++---
 man/BEDbase.Rd                 |  6 ++++--
 tests/testthat/test-bedbaser.R |  7 +++++++
 3 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/R/bedbaser.R b/R/bedbaser.R
index 10e1dbb..d236c94 100644
--- a/R/bedbaser.R
+++ b/R/bedbaser.R
@@ -40,6 +40,9 @@
 #'
 #' @param cache_path character(1) cache
 #' @param quietly logical(1) (default \code{FALSE}) display messages
+#' @param host character(1) (default \code{"api.bedbase.org"}) API host,
+#' e.g., a development or test server. Prefix with \code{http://} for a
+#' server without TLS.
 #'
 #' @return BEDbase object
 #'
@@ -49,7 +52,10 @@
 #' bb_metadata(bedbase, ex_bed$id)
 #'
 #' @export
-BEDbase <- function(cache_path, quietly = FALSE) {
+BEDbase <- function(cache_path, quietly = FALSE, host = "api.bedbase.org") {
+    stopifnot(is.character(host), length(host) == 1L, nzchar(host))
+    scheme <- if (startsWith(host, "http://")) "http" else "https"
+    host <- sub("^https?://", "", host)
     if (missing(cache_path)) {
         cache_path <- tools::R_user_dir("bedbaser", which = "cache")
     }
@@ -61,12 +67,13 @@ BEDbase <- function(cache_path, quietly = FALSE) {
             bedsets = BiocFileCache::BiocFileCache(bedsets_path, ask = FALSE),
             AnVIL::Service(
                 service = "bedbase",
-                host = "api.bedbase.org",
+                host = host,
                 api_reference_version = .BEDBASE_API_REFERENCE_VERSION,
                 authenticate = FALSE,
                 package = "bedbaser",
                 api_url = character(),
-                api_reference_url = "https://api.bedbase.org/v1/openapi.json",
+                schemes = scheme,
+                api_reference_url = paste0(scheme, "://", host, "/v1/openapi.json")
             )
         )
     )
diff --git a/man/BEDbase.Rd b/man/BEDbase.Rd
index a871a06..00a7a55 100644
--- a/man/BEDbase.Rd
+++ b/man/BEDbase.Rd
@@ -7,7 +7,7 @@
 \alias{setCache}
 \title{An R client for BEDbase}
 \usage{
-BEDbase(cache_path, quietly = FALSE)
+BEDbase(cache_path, quietly = FALSE, host = "api.bedbase.org")
 
 \S4method{show}{BEDbase}(object)
 
@@ -20,7 +20,9 @@ setCache(x, cache_path, quietly = TRUE)
 
 \item{quietly}{logical(1) (default \code{TRUE}) display messages}
 
-\item{object}{BEDbase() object}
+\item{host}{character(1) (default \code{"api.bedbase.org"}) API host,
+e.g., a development or test server. Prefix with \code{http://} for a
+server without TLS.}
 
 \item{x}{BEDbase() object}
 
diff --git a/tests/testthat/test-bedbaser.R b/tests/testthat/test-bedbaser.R
index 51803e5..c668a9d 100644
--- a/tests/testthat/test-bedbaser.R
+++ b/tests/testthat/test-bedbaser.R
@@ -191,3 +191,10 @@ test_that("show prints a summary", {
     expect_output(show(bedbase), "BEDbase client")
     expect_output(show(bedbase), "api.bedbase.org")
 })
+
+test_that("BEDbase host argument is used", {
+    expect_equal(bedbase@host, "api.bedbase.org")
+    with_scheme <- BEDbase(tempdir(), quietly = TRUE, host = "https://api.bedbase.org")
+    expect_equal(with_scheme@host, "api.bedbase.org")
+    expect_error(BEDbase(tempdir(), quietly = TRUE, host = ""))
+})