Move the check for subjects_dir (that is repeated across different files) into a function in functions.

This check uses `stat`, which works in different ways for macOS and linux.
Make the function (stat) work for both linux (GNU coreutils) and macOS (unclear version).

Author: dkuegler

long_fastsurfer.sh

@@ -223,20 +223,7 @@ if [ "${#tpids[@]}" -ne "${#t1s[@]}" ]
 fi
 
 # check that SUBJECTS_DIR exists
-if [[ -z "${sd}" ]]
-then
-  echo "ERROR: No subject directory defined via --sd. This is required!"
-  exit 1
-elif [[ ! -d "${sd}" ]]
-then
-  echo "INFO: The subject directory did not exist, creating it now."
-  if ! mkdir -p "$sd" ; then echo "ERROR: directory creation failed" ; exit 1; fi
-elif [[ "$(stat -c "%u:%g" "$sd")" == "0:0" ]] && [[ "$(id -u)" != "0" ]] && [[ "$(stat -c "%a" "$sd" | tail -c 2)" -lt 6 ]]
-then
-  echo "ERROR: The subject directory ($sd) is owned by root and is not writable. FastSurfer cannot write results! "
-  echo "  This can happen if the directory is created by docker. Make sure to create the directory before invoking docker!"
-  exit 1
-fi
+check_create_subjects_dir_properties "$sd"
 
 if [[ -z "$LF" ]] ; then LF="$sd/$tid/scripts/long_fastsurfer.log" ; fi
 # make sure the directory for the logfile exists, create automatically if the directory is not in $sd

recon_surf/functions.sh

@@ -18,6 +18,37 @@ if [ "${PIPESTATUS[0]}" -ne 0 ] ; then
 fi
 export timecmd
 
+function check_create_subjects_dir_properties()
+{
+  # 1: subjects_dir
+  if [[ -z "$1" ]]
+  then
+    echo "ERROR: No subject directory defined via --sd. This is required!"
+    exit 1
+  elif [[ ! -d "$1" ]]
+  then
+    echo "INFO: The subject directory did not exist, creating it now."
+    if [[ "$(id -u)" == 0 ]] ; then echo "WARNING: Creating as root!" ; fi
+    if ! mkdir -p "$1" ; then echo "ERROR: directory creation failed" ; exit 1; fi
+  else
+    if [[ "$(stat --version | head -n 1)" =~ GNU[[:space:]]coreutils ]] ; then # linux
+      user_group=$(stat -c "%u:%g" "$1")
+      world_access=$(stat -c "%a" "$1" | tail -c 2)
+    elif [[ "$(stat -- 2>&1 | tail -n 1)" =~ ^usage:[[:space:]]stat.*-f[[:space:]]format ]] ; then # macOS
+      user_group=$(stat -f "%u:%g" "$1")
+      world_access=$(stat -f "%p" "$1" | tail -c 2)
+    else echo "ERROR: Cannot detect stat interface!" ; exit 1
+    fi
+    if [[ "$user_group" == "0:0" ]] && [[ "$(id -u)" != "0" ]] && [[ "$world_access" -lt 6 ]]
+    then
+      echo "ERROR: The subject directory ($1) is owned by root and is not writable."
+      echo "  FastSurfer cannot write results! This can happen if the directory is created"
+      echo "  by docker. Make sure to create the directory before invoking docker!"
+      exit 1
+    fi
+  fi
+}
+
 function RunIt()
 {
   # parameters

recon_surf/long_prepare_template.sh

@@ -220,25 +220,7 @@ then
 fi
 
 # check that SUBJECTS_DIR exists
-if [[ -z "$SUBJECTS_DIR" ]]
-then
-  echo "ERROR: No subject directory defined via --sd. This is required!"
-  exit 1;
-fi
-if [[ ! -d "${sd}" ]]
-then
-  echo "INFO: The subject directory did not exist, creating it now."
-  if ! mkdir -p "$SUBJECTS_DIR" ; then echo "ERROR: directory creation failed" ; exit 1; fi
-fi
-if [[ "$(stat -c "%u:%g" "$SUBJECTS_DIR")" == "0:0" ]] && [[ "$(id -u)" != "0" ]] && \
-  [[ "$(stat -c "%a" "$SUBJECTS_DIR" | tail -c 2)" -lt 6 ]]
-then
-  echo "ERROR: The subject directory ($SUBJECTS_DIR) is owned by root and is not writable."
-  echo "  FastSurfer cannot write results! This can happen if the directory is created by"
-  echo "  docker. Make sure to create the directory before invoking docker!"
-  exit 1;
-fi
-
+check_create_subjects_dir_properties "$SUBJECTS_DIR"
 
 ################################## SETUP and LOGFILE ##############################
 

run_fastsurfer.sh

@@ -563,24 +563,7 @@ if [[ "$legacy_parallel_hemi" == 1 ]] ; then
   fi
 fi
 
-if [[ -z "${sd}" ]]
-then
-  echo "ERROR: No subject directory defined via --sd. This is required!"
-  exit 1
-fi
-if [[ ! -d "${sd}" ]]
-then
-  echo "INFO: The subject directory did not exist, creating it now." | tee -a "$tmpLF"
-  if ! mkdir -p "$sd" ; then echo "ERROR: Subject directory creation failed" ; exit 1 ; fi
-fi
-if [[ "$(stat -c "%u:%g" "$sd")" == "0:0" ]] && [[ "$(id -u)" != "0" ]] && \
-  [[ "$(stat -c "%a" "$sd" | tail -c 2)" -lt 6 ]]
-then
-  echo "ERROR: The subject directory ($sd) is owned by root and is not writable."
-  echo "  FastSurfer cannot write results! This can happen if the directory is created"
-  echo "  by docker. Make sure to create the directory before invoking docker!"
-  exit 1
-fi
+check_create_subjects_dir_properties "$sd"
 
 if [[ -z "$subject" ]]
 then

srun_fastsurfer.sh

@@ -383,6 +383,7 @@ do
   fi
 done
 debugf "$newline\n"
+# the following stat command is not compatible with macOS, but srun_fastsurfer is not expected to be
 shell=$(stat -c %N "/proc/$$/exe" | cut -d">" -f2 | tail -c +3 | head -c -2)
 debug "Running in shell $shell: $($shell --version 2>/dev/null | head -n 1)"
 debug ""