Fixed issue that appeared when trying to remove temporary folder from…

… different file systems (#2473)

* install_sct: replaced hard-coded bin by $BIN_DIR

* sct_download_data: Now copying folder instead of moving it

Also using distutils instead of shutil, to copy directories that might
not be empty.
Addressed issue #2472

* sct_download_data: No more removal of existing file in dest folder

install_sct

@@ -485,9 +485,9 @@ fi
 
 ## Create launchers for Python scripts
 echo -e "\nCreating launchers for Python scripts..."
-mkdir -p $SCT_DIR/bin
+mkdir -p $SCT_DIR/$BIN_DIR
 for file in $SCT_DIR/python/envs/venv_sct/bin/*sct*; do
- cp "$file" "$SCT_DIR/bin/"
+ cp "$file" "$SCT_DIR/$BIN_DIR/"
  res=$?
  if [[ $res != 0 ]]; then
  echo "\nProblem creating launchers!"
@@ -503,8 +503,8 @@ done
 
 ## Create symbolic links for Shell scripts (-f: overwrite if exists)
 echo -e "\nCreating symbolic links for Shell scripts..."
-ln -s -f $SCT_DIR/shell/sct_run_batch.sh $SCT_DIR/bin/sct_run_batch
-ln -s -f $SCT_DIR/shell/_run_with_log.sh $SCT_DIR/bin/_run_with_log.sh
+ln -s -f $SCT_DIR/shell/sct_run_batch.sh $SCT_DIR/$BIN_DIR/sct_run_batch
+ln -s -f $SCT_DIR/shell/_run_with_log.sh $SCT_DIR/$BIN_DIR/_run_with_log.sh
 res=$?
 if [[ $res != 0 ]]; then
  echo "\nProblem creating symlinks!"

scripts/sct_download_data.py

@@ -18,7 +18,8 @@
 import tarfile
 import tempfile
 import zipfile
-from shutil import rmtree, move, copytree
+from shutil import rmtree
+from distutils.dir_util import copy_tree
 
 import requests
 from requests.adapters import HTTPAdapter
@@ -144,24 +145,24 @@ def main(args=None):
  extracted_files_paths.append(os.path.join(os.path.abspath(dest_tmp_folder), extracted_file))
 
  # Check if files and folder already exists
- sct.printv('\nCheck if files or folder already exists on the destination path...', verbose)
+ sct.printv('\nCheck if folder already exists on the destination path...', verbose)
  for data_extracted_name in extracted_files:
  fullpath_dest = os.path.join(dest_folder, data_extracted_name)
  if os.path.isdir(fullpath_dest):
  sct.printv("Folder {} already exists. Removing it...".format(data_extracted_name), 1, 'warning')
  rmtree(fullpath_dest)
- elif os.path.isfile(fullpath_dest):
- sct.printv("File {} already exists. Removing it...".format(data_extracted_name), 1, 'warning')
- os.remove(fullpath_dest)
 
  # Destination path
- for source_path in extracted_files_paths:
- # Move the content of source to destination
- move(source_path, dest_folder, copy_function=copytree)
-
- sct.printv('\nRemove temporary files...', verbose)
- os.remove(tmp_file)
- rmtree(dest_tmp_folder)
+ # for source_path in extracted_files_paths:
+ # Copy the content of source to destination (and create destination folder)
+ copy_tree(dest_tmp_folder, dest_folder)
+
+ sct.printv("\nRemove temporary folders...", verbose)
+ try:
+ rmtree(os.path.split(tmp_file)[0])
+ rmtree(dest_tmp_folder)
+ except Exception as error:
+ print("Cannot remove temp folder: " + repr(error))
 
  sct.printv('Done!\n', verbose)
  return 0