From 8935b0b2a4c2a843361fd3a7f9f284c0261fb7c5 Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Wed, 11 Mar 2026 13:22:54 +0100
Subject: [PATCH] feat: allow passing of global settings launching from R or
 running docker container.

---
 NEWS.md                |   2 ++
 R/launch_FreesearchR.R |  28 +++++++++++++++++++++++-----
 R/sysdata.rda          | Bin 2838 -> 2661 bytes
 R/ui_elements.R        |   8 ++++----
 SESSION.md             |  19 -------------------
 5 files changed, 29 insertions(+), 28 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 6f50a612..7c44be1a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,6 +6,8 @@
 
 *NEW* New with_labels() function (and helpers) added to allow easy preservation of labels.
 
+*NEW* option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Docs will follow.
+
 # FreesearchR 26.3.1
 
 *FIX* ~~Include font files for static loading without dependency on Google.~~ Kept webfonts from google as local fonts are not working for now.
diff --git a/R/launch_FreesearchR.R b/R/launch_FreesearchR.R
index 504de474..469c443b 100644
--- a/R/launch_FreesearchR.R
+++ b/R/launch_FreesearchR.R
@@ -23,11 +23,11 @@ launch_FreesearchR <- function(inlcude_globalenv = TRUE,
                                data_limit_upper = 100000,
                                data_limit_lower = 1,
                                ...) {
-  global_freesearchR <- list(
-    include_globalenv = include_globalenv,
-    data_limit_default = data_limit_default,
-    data_limit_upper = data_limit_upper,
-    data_limit_lower = data_limit_lower
+  Sys.setenv(
+    INCLUDE_GLOBALENV = include_globalenv,
+    DATA_LIMIT_DEFAULT = data_limit_default,
+    DATA_LIMIT_UPPER = data_limit_upper,
+    DATA_LIMIT_LOWER = data_limit_lower
   )
 
   appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
@@ -39,3 +39,21 @@ launch_FreesearchR <- function(inlcude_globalenv = TRUE,
   a <- shiny::runApp(appDir = paste0(appDir, "/app.R"), ...)
   return(invisible(a))
 }
+
+
+## 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)
+
+  if (!is.na(val) && nzchar(val)) {
+    return(val)
+  }
+
+  # Fall back to default (can be overridden when launching from R)
+  if (!is.null(default)) {
+    return(default)
+  }
+
+  stop(paste("Required config variable not set:", var_name))
+}
diff --git a/R/sysdata.rda b/R/sysdata.rda
index e7ce41066e6125ce50acf9792d07bde50c433502..f20ba2552a749586b3c5f0ce62e1446fd82b4b4c 100644
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diff --git a/R/ui_elements.R b/R/ui_elements.R
index 0aea99e8..cac844a0 100644
--- a/R/ui_elements.R
+++ b/R/ui_elements.R
@@ -83,9 +83,9 @@ ui_elements <- function(selection) {
               layout_params = "dropdown",
               # title = "Choose a datafile to upload",
               file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta"),
-              limit_default = global_freesearchR$data_limit_default,
-              limit_lower = global_freesearchR$data_limit_lower,
-              limit_upper = global_freesearchR$data_limit_upper
+              limit_default = DATA_LIMIT_DEFAULT,
+              limit_lower = DATA_LIMIT_LOWER,
+              limit_upper = DATA_LIMIT_UPPER
 
             )
           ),
@@ -107,7 +107,7 @@ ui_elements <- function(selection) {
               id = "env",
               title = NULL,
               packages = c("NHANES", "stRoke", "datasets", "MASS"),
-              globalenv = global_freesearchR$include_globalenv
+              globalenv = isTruthy(INCLUDE_GLOBALENV)
             )
           ),
           # shiny::conditionalPanel(
diff --git a/SESSION.md b/SESSION.md
index 608dbe98..1193d865 100644
--- a/SESSION.md
+++ b/SESSION.md
@@ -26,8 +26,6 @@
 |apexcharter       |0.4.5         |2026-01-07 |CRAN (R 4.5.2) |
 |askpass           |1.2.1         |2024-10-04 |CRAN (R 4.5.0) |
 |assertthat        |0.2.1         |2019-03-21 |CRAN (R 4.5.0) |
-|attachment        |0.4.5         |2025-03-14 |CRAN (R 4.5.0) |
-|attempt           |0.3.1         |2020-05-03 |CRAN (R 4.5.0) |
 |backports         |1.5.0         |2024-05-23 |CRAN (R 4.5.0) |
 |base64enc         |0.1-6         |2026-02-02 |CRAN (R 4.5.2) |
 |bayestestR        |0.17.0        |2025-08-29 |CRAN (R 4.5.0) |
@@ -46,7 +44,6 @@
 |cardx             |0.3.2         |2026-02-05 |CRAN (R 4.5.2) |
 |caTools           |1.18.3        |2024-09-04 |CRAN (R 4.5.0) |
 |cellranger        |1.1.0         |2016-07-27 |CRAN (R 4.5.0) |
-|cffr              |1.2.1         |2026-01-12 |CRAN (R 4.5.2) |
 |checkmate         |2.3.4         |2026-02-03 |CRAN (R 4.5.2) |
 |class             |7.3-23        |2025-01-01 |CRAN (R 4.5.2) |
 |classInt          |0.4-11        |2025-01-08 |CRAN (R 4.5.0) |
@@ -56,8 +53,6 @@
 |colorspace        |2.1-2         |2025-09-22 |CRAN (R 4.5.0) |
 |commonmark        |2.0.0         |2025-07-07 |CRAN (R 4.5.0) |
 |crayon            |1.5.3         |2024-06-20 |CRAN (R 4.5.0) |
-|credentials       |2.0.3         |2025-09-12 |CRAN (R 4.5.0) |
-|curl              |7.0.0         |2025-08-19 |CRAN (R 4.5.0) |
 |data.table        |1.18.2.1      |2026-01-27 |CRAN (R 4.5.2) |
 |datamods          |1.5.3         |2024-10-02 |CRAN (R 4.5.0) |
 |datawizard        |1.3.0         |2025-10-11 |CRAN (R 4.5.0) |
@@ -66,7 +61,6 @@
 |devtools          |2.4.6         |2025-10-03 |CRAN (R 4.5.0) |
 |DHARMa            |0.4.7         |2024-10-18 |CRAN (R 4.5.0) |
 |digest            |0.6.39        |2025-11-19 |CRAN (R 4.5.2) |
-|dockerfiler       |0.2.5         |2025-05-07 |CRAN (R 4.5.0) |
 |doParallel        |1.0.17        |2022-02-07 |CRAN (R 4.5.0) |
 |dplyr             |1.2.0         |2026-02-03 |CRAN (R 4.5.2) |
 |DT                |0.34.0        |2025-09-02 |CRAN (R 4.5.0) |
@@ -93,15 +87,12 @@
 |fs                |1.6.6         |2025-04-12 |CRAN (R 4.5.0) |
 |gdtools           |0.5.0         |2026-02-09 |CRAN (R 4.5.2) |
 |generics          |0.1.4         |2025-05-09 |CRAN (R 4.5.0) |
-|gert              |2.3.1         |2026-01-11 |CRAN (R 4.5.2) |
 |ggalluvial        |0.12.5        |2023-02-22 |CRAN (R 4.5.0) |
 |ggcorrplot        |0.1.4.1       |2023-09-05 |CRAN (R 4.5.0) |
 |ggforce           |0.5.0         |2025-06-18 |CRAN (R 4.5.0) |
 |ggplot2           |4.0.2         |2026-02-03 |CRAN (R 4.5.2) |
 |ggridges          |0.5.7         |2025-08-27 |CRAN (R 4.5.0) |
 |ggstats           |0.12.0        |2025-12-22 |CRAN (R 4.5.2) |
-|gh                |1.5.0         |2025-05-26 |CRAN (R 4.5.0) |
-|gitcreds          |0.1.2         |2022-09-08 |CRAN (R 4.5.0) |
 |glue              |1.8.0         |2024-09-30 |CRAN (R 4.5.0) |
 |gridExtra         |2.3           |2017-09-09 |CRAN (R 4.5.0) |
 |gt                |1.3.0         |2026-01-22 |CRAN (R 4.5.2) |
@@ -115,24 +106,20 @@
 |htmltools         |0.5.9         |2025-12-04 |CRAN (R 4.5.2) |
 |htmlwidgets       |1.6.4         |2023-12-06 |CRAN (R 4.5.0) |
 |httpuv            |1.6.16        |2025-04-16 |CRAN (R 4.5.0) |
-|httr2             |1.2.2         |2025-12-08 |CRAN (R 4.5.2) |
 |IDEAFilter        |0.2.1         |2025-07-29 |CRAN (R 4.5.0) |
 |insight           |1.4.6         |2026-02-04 |CRAN (R 4.5.2) |
 |iterators         |1.0.14        |2022-02-05 |CRAN (R 4.5.0) |
 |jquerylib         |0.1.4         |2021-04-26 |CRAN (R 4.5.0) |
 |jsonlite          |2.0.0         |2025-03-27 |CRAN (R 4.5.0) |
-|jsonvalidate      |1.5.0         |2025-02-07 |CRAN (R 4.5.0) |
 |KernSmooth        |2.23-26       |2025-01-01 |CRAN (R 4.5.2) |
 |keyring           |1.4.1         |2025-06-15 |CRAN (R 4.5.0) |
 |knitr             |1.51          |2025-12-20 |CRAN (R 4.5.2) |
 |later             |1.4.6         |2026-02-13 |CRAN (R 4.5.2) |
 |lattice           |0.22-7        |2025-04-02 |CRAN (R 4.5.2) |
 |lifecycle         |1.0.5         |2026-01-08 |CRAN (R 4.5.2) |
-|litedown          |0.9           |2025-12-18 |CRAN (R 4.5.2) |
 |lme4              |1.1-38        |2025-12-02 |CRAN (R 4.5.2) |
 |lubridate         |1.9.5         |2026-02-04 |CRAN (R 4.5.2) |
 |magrittr          |2.0.4         |2025-09-12 |CRAN (R 4.5.0) |
-|markdown          |2.0           |2025-03-23 |CRAN (R 4.5.0) |
 |MASS              |7.3-65        |2025-02-28 |CRAN (R 4.5.0) |
 |Matrix            |1.7-4         |2025-08-28 |CRAN (R 4.5.2) |
 |memoise           |2.0.1         |2021-11-26 |CRAN (R 4.5.0) |
@@ -148,7 +135,6 @@
 |openssl           |2.3.4         |2025-09-30 |CRAN (R 4.5.0) |
 |openxlsx2         |1.23.1        |2026-01-19 |CRAN (R 4.5.2) |
 |otel              |0.2.0         |2025-08-29 |CRAN (R 4.5.0) |
-|pak               |0.9.2         |2025-12-22 |CRAN (R 4.5.2) |
 |parameters        |0.28.3        |2025-11-25 |CRAN (R 4.5.2) |
 |patchwork         |1.3.2         |2025-08-25 |CRAN (R 4.5.0) |
 |pbmcapply         |1.5.1         |2022-04-28 |CRAN (R 4.5.0) |
@@ -172,7 +158,6 @@
 |R6                |2.6.1         |2025-02-15 |CRAN (R 4.5.0) |
 |ragg              |1.5.0         |2025-09-02 |CRAN (R 4.5.0) |
 |rankinPlot        |1.1.0         |2023-01-30 |CRAN (R 4.5.0) |
-|rappdirs          |0.3.4         |2026-01-17 |CRAN (R 4.5.2) |
 |rbibutils         |2.4.1         |2026-01-21 |CRAN (R 4.5.2) |
 |RColorBrewer      |1.1-3         |2022-04-03 |CRAN (R 4.5.0) |
 |Rcpp              |1.1.1         |2026-01-10 |CRAN (R 4.5.2) |
@@ -205,7 +190,6 @@
 |sessioninfo       |1.2.3         |2025-02-05 |CRAN (R 4.5.0) |
 |shiny             |1.13.0        |2026-02-20 |CRAN (R 4.5.2) |
 |shiny.i18n        |0.3.0         |2023-01-16 |CRAN (R 4.5.0) |
-|shiny2docker      |0.0.3         |2025-06-28 |CRAN (R 4.5.0) |
 |shinybusy         |0.3.3         |2024-03-09 |CRAN (R 4.5.0) |
 |shinyjs           |2.1.1         |2026-01-15 |CRAN (R 4.5.2) |
 |shinyTime         |1.0.3         |2022-08-19 |CRAN (R 4.5.0) |
@@ -214,7 +198,6 @@
 |stringi           |1.8.7         |2025-03-27 |CRAN (R 4.5.0) |
 |stringr           |1.6.0         |2025-11-04 |CRAN (R 4.5.0) |
 |stRoke            |25.9.2        |2025-09-30 |CRAN (R 4.5.0) |
-|sys               |3.4.3         |2024-10-04 |CRAN (R 4.5.0) |
 |systemfonts       |1.3.1         |2025-10-01 |CRAN (R 4.5.0) |
 |testthat          |3.3.2         |2026-01-11 |CRAN (R 4.5.2) |
 |textshaping       |1.0.4         |2025-10-10 |CRAN (R 4.5.0) |
@@ -229,7 +212,6 @@
 |tzdb              |0.5.0         |2025-03-15 |CRAN (R 4.5.0) |
 |usethis           |3.2.1         |2025-09-06 |CRAN (R 4.5.0) |
 |uuid              |1.2-2         |2026-01-23 |CRAN (R 4.5.2) |
-|V8                |8.0.1         |2025-10-10 |CRAN (R 4.5.0) |
 |vctrs             |0.7.1         |2026-01-23 |CRAN (R 4.5.2) |
 |viridis           |0.6.5         |2024-01-29 |CRAN (R 4.5.0) |
 |viridisLite       |0.4.3         |2026-02-04 |CRAN (R 4.5.2) |
@@ -240,5 +222,4 @@
 |xml2              |1.5.2         |2026-01-17 |CRAN (R 4.5.2) |
 |xtable            |1.8-4         |2019-04-21 |CRAN (R 4.5.0) |
 |yaml              |2.3.12        |2025-12-10 |CRAN (R 4.5.2) |
-|yesno             |0.1.3         |2024-07-26 |CRAN (R 4.5.0) |
 |zip               |2.3.3         |2025-05-13 |CRAN (R 4.5.0) |