From 95fc0a4d5f3a731583eec6f5c3fdab73f3634715 Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Thu, 12 Mar 2026 11:32:06 +0100
Subject: [PATCH] fix: trying to fix launching with globals

---
 R/hosted_version.R        |  2 +-
 R/launch_FreesearchR.R    | 19 +++++++++++++++----
 man/launch_FreesearchR.Rd |  8 ++++----
 3 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/R/hosted_version.R b/R/hosted_version.R
index 2306a9f6..b15a5737 100644
--- a/R/hosted_version.R
+++ b/R/hosted_version.R
@@ -1 +1 @@
-hosted_version <- function()'v26.3.3-260311'
+hosted_version <- function()'v26.3.3-260312'
diff --git a/R/launch_FreesearchR.R b/R/launch_FreesearchR.R
index 99046649..a789f185 100644
--- a/R/launch_FreesearchR.R
+++ b/R/launch_FreesearchR.R
@@ -43,14 +43,15 @@ launch_FreesearchR <- function(include_globalenv = TRUE,
 
 ## Helper to set env variables
 get_config <- function(var_name, default = NULL) {
-  # First check environment variables (set by Docker)
-  val <- Sys.getenv(var_name, unset = NA)
+  val <- Sys.getenv(var_name, unset = NA_character_)
 
-  if (!is.na(val) && nzchar(val)) {
+  # Only use env var if it is explicitly set and non-empty
+  if (!is.na(val) && nzchar(trimws(val))) {
+    if (is.logical(default)) return(to_logical(val))
+    if (is.numeric(default)) return(as.numeric(val))
     return(val)
   }
 
-  # Fall back to default (can be overridden when launching from R)
   if (!is.null(default)) {
     return(default)
   }
@@ -58,6 +59,16 @@ get_config <- function(var_name, default = NULL) {
   stop(paste("Required config variable not set:", var_name))
 }
 
+to_logical <- function(x) {
+  result <- switch(tolower(trimws(as.character(x))),
+                   "true"  = , "1" = , "yes" = TRUE,
+                   "false" = , "0" = , "no"  = FALSE,
+                   NA
+  )
+  if (is.na(result)) stop(paste("Cannot coerce to logical:", x))
+  result
+}
+
 
 ## File loader - based on the module, uses hard coded default values
 load_file <- function(path) {
diff --git a/man/launch_FreesearchR.Rd b/man/launch_FreesearchR.Rd
index e052ba7b..2ab6c607 100644
--- a/man/launch_FreesearchR.Rd
+++ b/man/launch_FreesearchR.Rd
@@ -5,7 +5,7 @@
 \title{Easily launch the FreesearchR app}
 \usage{
 launch_FreesearchR(
-  inlcude_globalenv = TRUE,
+  include_globalenv = TRUE,
   data_limit_default = 1000,
   data_limit_upper = 1e+05,
   data_limit_lower = 1,
@@ -13,6 +13,9 @@ launch_FreesearchR(
 )
 }
 \arguments{
+\item{include_globalenv}{flag to include global env (local data) as option
+when loading data}
+
 \item{data_limit_default}{default data set observations limit}
 
 \item{data_limit_upper}{data set observations upper limit}
@@ -20,9 +23,6 @@ launch_FreesearchR(
 \item{data_limit_lower}{data set observations lower limit}
 
 \item{...}{passed on to \code{shiny::runApp()}}
-
-\item{include_globalenv}{flag to include global env (local data) as option
-when loading data}
 }
 \value{
 shiny app