Fix: symlink may point to absolute path

recon_surf/functions.sh

@@ -225,15 +225,16 @@ function check_allow_root()
 
 function softlink_or_copy()
 {
+  # Creates a symlink at file pointing to target; if that fails, for example because symlinks are not supported by the
+  # file system, copy the file instead. The baseline call is `ln -sf $1 $2 >> $3`.
   # params
-  # 1: file
-  # 2: target
+  # 1: link target (or file copy source) -> path to target of link / absolute or relative but relative to **file**!!
+  # 2: link (or file copy destination) -> path to link file / absolute or relative to cwd
   # 3: logfile
   # 4: cmdf
-  local LF="$3"
-  local ln_cmd=(ln -sf "$1" "$2")
-  local cp_cmd=(cp "$1" "$2")
+  local LF="$3" link_tgt_cp_src="$1" link_cp_dest="$2"
   if [[ $# -lt 3 ]] || [[ -z "$LF" ]] ; then echo "WARNING: Parameter 3 of softlink_or_copy missing!" ; fi
+  local ln_cmd=(ln -sf "$link_tgt_cp_src" "$link_cp_dest")
   if [[ $# -eq 4 ]]
   then
     local CMDF=$4
@@ -242,8 +243,13 @@ function softlink_or_copy()
       echo "$timecmd $(echo_quoted "${ln_cmd[@]}")"
       echo "if [[ \${PIPESTATUS[0]} != 0 ]]"
       echo "then"
-      echo "  echo $(echo_quoted "${cp_cmd[@]}")"
-      echo "  $timecmd $(echo_quoted "${cp_cmd[@]}")"
+      if [[ "$link_tgt_cp_src" != /* ]] ; then # relative path, defined with respect to $link_cp_dest
+        echo "  src=\$(dirname $(echo_quoted "$link_cp_dest"))/$(echo_quoted "$link_tgt_cp_src")"
+      else
+        echo "  src=$(echo_quoted "$link_tgt_cp_src")"
+      fi
+      echo "  echo \"cp \\\"\$src\\\" $(echo_quoted "$link_cp_dest")\""
+      echo "  $timecmd cp \"\$src\" $(echo_quoted "$link_cp_dest")"
       echo "  if [[ \${PIPESTATUS[0]} != 0 ]] ; then exit 1 ; fi"
       echo "fi"
     } | tee -a "$CMDF"
@@ -253,15 +259,29 @@ function softlink_or_copy()
       $timecmd "${ln_cmd[@]}" 2>&1
       if [[ "${PIPESTATUS[0]}" != 0 ]]
       then
-        echo_quoted "${cp_cmd[@]}"
-        $timecmd "${cp_cmd[@]}" 2>&1
+        if [[ "$link_tgt_cp_src" != /* ]] ; then link_tgt_cp_src="$(dirname "$2")/$link_tgt_cp_src" ; fi # relative path
+        echo_quoted "cp" "$link_tgt_cp_src" "$link_cp_dest"
+        $timecmd "cp" "$link_tgt_cp_src" "$link_cp_dest" 2>&1
         if [[ "${PIPESTATUS[0]}" != 0 ]] ; then exit 1 ; fi
       fi
     } | tee -a "$LF"
     if [[ "${PIPESTATUS[0]}" != 0 ]]; then exit 1; fi # forward subshell exit to main script
   fi
 }
 
+function relative_to()
+{
+  # Generate a relative path from $2 to $3, so `ln -s $(relative_to python /path/src /path/target) /path/src` is valid.
+  # params
+  # $1: python executable
+  # $2: base path whose directory is used as the starting point (e.g., the link path; start dir is dirname($2))
+  # $3: target path to compute the relative path to (normal shell quoting is allowed)
+  script=('import sys, os'
+          'base, target = sys.argv[sys.argv.index("-c")+1:]'
+          'print(os.path.relpath(target, start=os.path.dirname(base)))')
+  $1 -c "$(printf "%s\n" "${script[@]}")" "$2" "$3"
+}
+
 function echo_quoted()
 {
   # params ... 1-N

run_fastsurfer.sh

@@ -1102,7 +1102,13 @@ then
         exit 1
       fi
       # create a symlink of the stats file for the old file name
-      softlink_or_copy "$asegdkt_vinn_statsfile" "$asegdkt_statsfile" "$seg_log"
+      # at this point, $asegdkt_vinn_statsfile might be an absolute path, which causes problems in containers, so make
+      # the path relative, if both statsfiles are in $subject_dir (which will be almost always).
+      if [[ "$asegdkt_vinn_statsfile" == "$subject_dir/"* ]] && [[ "$asegdkt_statsfile" == "$subject_dir/"* ]]
+      then asegdkt_vinn_statsfile_=$(relative_to "$python" "$asegdkt_statsfile" "$asegdkt_vinn_statsfile")
+      else asegdkt_vinn_statsfile_=$asegdkt_vinn_statsfile
+      fi
+      softlink_or_copy "$asegdkt_vinn_statsfile_" "$asegdkt_statsfile" "$seg_log"
       # create the aseg only statsfile
       mask_name_manedit=$(add_file_suffix "$mask_name" "manedit")
       if [[ -e "$mask_name_manedit" ]] ; then mask_name="$mask_name_manedit" ; fi