From 2e660cac9a0e0c01b48f154d395852345e1355da Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 1 Aug 2024 15:40:56 +0100
Subject: [PATCH] JAL-3631 Convert both CLASSPATHS in update.sh

---
 utils/getdown/bin/jalview.ps1 |    2 +-
 utils/getdown/bin/update.sh   |   62 ++++++++++++++++++++++-------------------
 2 files changed, 35 insertions(+), 29 deletions(-)

diff --git a/utils/getdown/bin/jalview.ps1 b/utils/getdown/bin/jalview.ps1
index edf0e49..382b22e 100755
--- a/utils/getdown/bin/jalview.ps1
+++ b/utils/getdown/bin/jalview.ps1
@@ -66,7 +66,7 @@ function Readlink-f {
       If ( $( Split-Path -Path $target -IsAbsolute ) ) {
         $file = Get-Item -Path $target
       } Else {
-# symbolic link is relative: combine previous link parent dir with the link target and resolve
+        # symbolic link is relative: combine previous link parent dir with the link target and resolve
         $file = Get-Item -Path ( Join-Path -Path ( Split-Path -Path $prevfile -Parent ) -ChildPath $target -Resolve )
       }
     }
diff --git a/utils/getdown/bin/update.sh b/utils/getdown/bin/update.sh
index 92c28c2..9b9d2ac 100755
--- a/utils/getdown/bin/update.sh
+++ b/utils/getdown/bin/update.sh
@@ -2,6 +2,32 @@
 
 declare -a ARGS=("${@}")
 
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+  ISMACOS=1
+fi
+
+DEBUG=0
+USERSPACE=0
+INSTALLATION=0
+for RAWARG in "${@}"; do
+  ARG="${RAWARG%%=*}"
+  case "${ARG}" in
+    --debug)
+      DEBUG=1
+      ;;
+    --installation)
+      INSTALLATION=1
+      ;;
+    --userspace)
+      USERSPACE=1
+      ;;
+    *)
+      echo "Unknown option '${ARG}'.  Please use either --installation or --userspace." >&2
+      exit 2
+  esac
+done
+
 # this whole next part is because there's no readlink -f in Darwin
 function readlinkf() {
   FINDFILE="$1"
@@ -30,32 +56,6 @@ function readlinkf() {
   echo "${FILE}"
 }
 
-ISMACOS=0
-if [ "$( uname -s )" = "Darwin" ]; then
-  ISMACOS=1
-fi
-
-DEBUG=0
-USERSPACE=0
-INSTALLATION=0
-for RAWARG in "${@}"; do
-  ARG="${RAWARG%%=*}"
-  case "${ARG}" in
-    --debug)
-      DEBUG=1
-      ;;
-    --installation)
-      INSTALLATION=1
-      ;;
-    --userspace)
-      USERSPACE=1
-      ;;
-    *)
-      echo "Unkown option '${ARG}'" >&2
-      exit 2
-  esac
-done
-
 # args for the JVM
 declare -a JVMARGS=()
 
@@ -183,15 +183,21 @@ GDL_ARGS=( "${GDL_ARGS[@]}" "--headless" "--quit" "--nojavaconsole" "--nosplash"
 # change paths for Cygwin or WSL
 if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
   if [ "$(uname -o)" = "Cygwin" ]; then
-  # CYGWIN
+    # CYGWIN
     GDL_CLASSPATH=$(cygpath -pw "${GDL_CLASSPATH}")
+    GDC_CLASSPATH=$(cygpath -pw "${GDC_CLASSPATH}")
   elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
-  # WSL
+    # WSL
     GDL_CLASSPATH=""
     for JARPATH in "${GDL_JARPATHS[@]}"; do
       [ -n "${GDL_CLASSPATH}" ] && GDL_CLASSPATH="${GDL_CLASSPATH};"
       GDL_CLASSPATH="${GDL_CLASSPATH}$(wslpath -aw "${JARPATH}")"
     done
+    GDC_CLASSPATH=""
+    for JARPATH in "${GDC_JARPATHS[@]}"; do
+      [ -n "${GDC_CLASSPATH}" ] && GDC_CLASSPATH="${GDC_CLASSPATH};"
+      GDC_CLASSPATH="${GDC_CLASSPATH}$(wslpath -aw "${JARPATH}")"
+    done
     JAVA="${JAVA}.exe"
     SYSJAVA="java.exe"
   fi
-- 
1.7.10.2