From 7fd73a8a53792accf8897665270ae89c0f1a39bf Mon Sep 17 00:00:00 2001
From: Simon Li <spli@dundee.ac.uk>
Date: Wed, 19 Jun 2024 12:57:09 +0100
Subject: [PATCH] Add `CONDA_PROXY_SERVER` and `CRAN_PROXY_SERVER` private_env

This means installing conda and RStudio will not automatically configure a default server which is only useful for HIC-TRE images.
---
 modules/conda-setup.sh |  9 ++++++---
 modules/conda.ps1      | 14 +++++++++-----
 modules/rstudio.ps1    | 17 ++++++++++++-----
 modules/rstudio.sh     | 16 ++++++++++------
 templates/default.j2   |  6 ++++++
 5 files changed, 43 insertions(+), 19 deletions(-)

diff --git a/modules/conda-setup.sh b/modules/conda-setup.sh
index e408983..2f84160 100644
--- a/modules/conda-setup.sh
+++ b/modules/conda-setup.sh
@@ -29,9 +29,12 @@ for env in "${SETUPDIR}"/conda-environment*.yml ; do
     ~/conda/bin/mamba env update --file "$env"
 done
 
-echo "Setting default conda channel"
-cat > "$HOME/.condarc" <<EOF
+# Internal Conda proxy or repository
+if [ -n "${CONDA_PROXY_SERVER:-}" ]; then
+    echo "Configuring Conda proxy ${CONDA_PROXY_SERVER}"
+    cat > "$HOME/.condarc" <<EOF
 channels:
   - conda-forge
-channel_alias: http://conda.hic-tre.dundee.ac.uk
+channel_alias: ${CONDA_PROXY_SERVER}
 EOF
+fi
diff --git a/modules/conda.ps1 b/modules/conda.ps1
index 90ada5b..e52b095 100644
--- a/modules/conda.ps1
+++ b/modules/conda.ps1
@@ -40,10 +40,14 @@ if ( Test-Path -Path ${BASE_ENVIRONMENT_YML} -PathType Leaf ) {
     Write-Output "$BASE_ENVIRONMENT_YML not found, skipping"
 }
 
-$condarc = "C:\Users\Administrator\.condarc"
-New-Item $condarc
-Set-Content $condarc "channels:"
-Add-Content $condarc "  - conda-forge"
-Add-Content $condarc "channel_alias: http://conda.hic-tre.dundee.ac.uk"
+# Internal Conda proxy or repository
+if ( $Env:CONDA_PROXY_SERVER ) {
+    Write-Output "Configuring conda proxy ${Env:CONDA_PROXY_SERVER}"
+    $condarc = "C:\Users\Administrator\.condarc"
+    New-Item $condarc
+    Set-Content $condarc "channels:"
+    Add-Content $condarc "  - conda-forge"
+    Add-Content $condarc "channel_alias: ${Env:CONDA_PROXY_SERVER}"
+}
 
 conda deactivate
diff --git a/modules/rstudio.ps1 b/modules/rstudio.ps1
index bda50df..b7459be 100644
--- a/modules/rstudio.ps1
+++ b/modules/rstudio.ps1
@@ -25,14 +25,21 @@ $RConfig = @"
 # Set the default help type
 options(help_type="html")
 
-# HIC TRE R Repository
+# Set timezone
+Sys.setenv(TZ='Europe/London')
+
+"@
+
+# Internal CRAN proxy or repository
+if ( $Env:CRAN_PROXY_SERVER ) {
+  Write-Output "Configuring CRAN proxy ${Env:CRAN_PROXY_SERVER}"
+  $RConfig += @"
 local({r <- getOption("repos")
-       r["CRAN"] <- "http://cran.hic-tre.dundee.ac.uk/"
+       r["CRAN"] <- "${Env:CRAN_PROXY_SERVER}"
        options(repos=r)
 })
-
-# Set timezone
-Sys.setenv(TZ='Europe/London')
 "@
+}
+
 Set-Content "C:\Program Files\R\R-4.4.0\etc\Rprofile.site" $RConfig
 Set-Content "C:\Users\Administrator\Documents\.Renviron" "RSTUDIO_DISABLE_SECURE_DOWNLOAD_WARNING=1"
diff --git a/modules/rstudio.sh b/modules/rstudio.sh
index c3c116b..959de30 100644
--- a/modules/rstudio.sh
+++ b/modules/rstudio.sh
@@ -42,16 +42,20 @@ cat > "$HOME/.Rprofile" <<EOF
 # Set the default help type
 options(help_type="html")
 
-# HIC TRE R Repository
-local({r <- getOption("repos")
-       r["CRAN"] <- "http://cran.hic-tre.dundee.ac.uk/"
-       options(repos=r)
-})
-
 # Set timezone
 Sys.setenv(TZ='Europe/London')
 EOF
 
+# Internal CRAN proxy or repository
+if [ -n "${CRAN_PROXY_SERVER:-}" ]; then
+    echo "Configuring CRAN proxy ${CRAN_PROXY_SERVER}"
+cat >> "$HOME/.Rprofile" <<EOF
+local({r <- getOption("repos")
+    r["CRAN"] <- "$CRAN_PROXY_SERVER"
+    options(repos=r)
+})
+EOF
+
 echo "RSTUDIO_DISABLE_SECURE_DOWNLOAD_WARNING=1" >> "$HOME/.Renviron"
 
 sudo add-apt-repository -y ppa:c2d4u.team/c2d4u4.0+
diff --git a/templates/default.j2 b/templates/default.j2
index 2056a8f..19c2cb3 100644
--- a/templates/default.j2
+++ b/templates/default.j2
@@ -6,6 +6,12 @@
 
 {% set env = env|default([],true) %}
 {% set private_env = private_env|default([],true) %}
+{# For example, to configure an internal CRAN and conda proxy/repository:
+{% set private_env = [
+  "CONDA_PROXY_SERVER=http://conda.hic-tre.dundee.ac.uk",
+  "CRAN_PROXY_SERVER=http://cran.hic-tre.dundee.ac.uk/",
+] %}
+#}
 
 {% set modules = modules|default([],true) %}
 {% set security_modules = security_modules|default([],true) %}