From ec4d1a9d385baab1cf63a6ff0924051620b0bae3 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 30 Mar 2021 01:43:52 +0100
Subject: [PATCH] JAL-3830 Follow all SymbolicLinks in Windows powershell
 wrapper

---
 utils/getdown/bin/jalview.ps1 |   45 +++++++++++++++++++++++++++++++++++++----
 1 file changed, 41 insertions(+), 4 deletions(-)

diff --git a/utils/getdown/bin/jalview.ps1 b/utils/getdown/bin/jalview.ps1
index b84e275..7ae9a57 100755
--- a/utils/getdown/bin/jalview.ps1
+++ b/utils/getdown/bin/jalview.ps1
@@ -16,9 +16,46 @@ if ( $IsWindows -eq $null ) {
   $myIsMacOS = $IsMacOS
 }
 
-# parent dir of this script (should be the getdown app dir). Follow symlinks.
-$TARGET = ( Get-Item $MyInvocation.MyCommand.Path ).Target
-$DIR = If ( $TARGET -eq $null -or $TARGET.LinkType -ne "SymbolicLink" ) { Split-Path -Path $MyInvocation.MyCommand.Path -Parent } Else { Split-Path -Path $TARGET -Parent }
+# parent dir of this actual script (which should be the getdown appdir/bin). Follow all symlinks.  Like GNU readlink -f
+function Readlink-f {
+  Param($Link)
+  $Return = $null
+  $c = 0
+  $max = 100 # just in case we end up in a loop
+  [bool] $found = 0
+  $file = Get-Item -Path $Link
+  $prevfile = $null
+  While ( $c -lt $max -and "${file}" -ne "${prevfile}" -and -not $found ) {
+    $prevfile = $file
+    [string] $target = ( $file ).Target
+    If ( $target -eq $null -or ( $file ).LinkType -ne "SymbolicLink" ) {
+      $Return = $file
+      $found = 1
+    } Else {
+      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
+        $file = Get-Item -Path ( Join-Path -Path ( Split-Path -Path $prevfile -Parent ) -ChildPath $target -Resolve )
+      }
+    }
+    $c++
+  }
+  if ( -not $found ) {
+    throw "Could not determine path to actual file $( Split-Path -Path $Link -Leaf )"
+  }
+  $Return
+}
+
+# Avert problem with unix version of powershell and tell user the reason (Windows must always have .ps1 extension)
+if ( $MyInvocation.MyCommand.Path -eq $null ) {
+  throw "Script or link to script must have extension .ps1"
+}
+
+
+$CMDPATH = ( Get-Item $MyInvocation.MyCommand.Path )
+$SCRIPTPATH = Readlink-f -Link $CMDPATH
+$DIR = Split-Path -Path $SCRIPTPATH -Parent
 
 # set the "-open" parameter if myArg1 is non-zero-length, and not "open" or starts with a "-"
 $OPEN = ""
@@ -33,7 +70,7 @@ $GETDOWNTXT = Join-Path -Path $APPDIR -ChildPath "getdown.txt"
 
 # look for getdown.txt -- needed to create classpath
 if ( -not ( Test-Path -Path "${GETDOWNTXT}" ) ) {
-  throw "Cannot find getdown.txt"
+  throw "Cannot find ${GETDOWNTXT}"
 }
 
 # look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
-- 
1.7.10.2