Build branch craftbox/v0.3 with version v0.3.2 to craftbox on branch v0.3 (7d520dc)

Build pipeline: viash-hub.craftbox.v0.3.2-tpktm

Source commit: 7d520dc76c

Source message: Bump version to v0.3.2

src/move_files_to_directory/config.vsh.yaml

@@ -1,39 +1,52 @@
 name: move_files_to_directory
-summary: Publish one or multiple files to the same directory
-description: This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.
+summary: Publish one or multiple files or directories to the same output directory.
+description: |
+  This component copies one or multiple files or directories
+  to the same destination directory, creating the output directory if it doesn't
+  exist.
 authors:
   - __merge__: /src/_authors/dorien_roosen.yaml
     roles: [ maintainer ]
-arguments:
-  - name: "--input"
-    type: file
-    direction: input
-    required: true
-    multiple: true
-    description: Paths of the files that will be copied into the output directory.
-  - name: "--output"
-    type: file
-    direction: output
-    required: true
-    description: Path to output directory
-  - name: "--keep_symbolic_links"
-    alternatives: [-d]
-    type: boolean_true
-    description: Preserve symbolic links.
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--input"
+        type: file
+        direction: input
+        required: true
+        multiple: true
+        description: Paths of the files or directories that will be copied into the output directory.
+  - name: Outputs
+    arguments:
+      - name: "--output"
+        type: file
+        direction: output
+        required: true
+        description: Path to output directory.
+  - name: Options
+    arguments:
+      - name: "--keep_symbolic_links"
+        type: boolean_true
+        description: When set, symbolic links are preserved as symbolic links in the output directory. By default, symbolic links are dereferenced and the target file is copied.
+
 resources:
   - type: bash_script
     path: script.sh
+
 test_resources:
   - type: bash_script
     path: test.sh
 
 engines:
-- type: docker
-  image: debian:latest
-  setup:
+  - type: docker
+    image: debian:latest
+    setup:
       - type: apt
-        packages: [procps]
+        packages:
+          - procps
+  - type: native
 
 runners:
-- type: executable
-- type: nextflow
+  - type: executable
+  - type: nextflow

src/move_files_to_directory/script.sh

@@ -3,30 +3,37 @@
 set -eo pipefail
 
 ## VIASH START
-par_input="input.txt;input_2.txt"
+par_input="input.txt;input_dir.zarr"
 par_output="output"
+par_keep_symbolic_links="false"
 ## VIASH END
 
-
 if [[ ! -d "$par_output" ]]; then
   mkdir -p "$par_output"
 fi
 
-extra_params=( )
-
-if [ "$par_keep_symbolic_links" == "true" ]; then
-  extra_params+=( "-d" )
+# Set copy flags based on options
+if [[ "$par_keep_symbolic_links" == "true" ]]; then
+  # -a implies -dR --preserve=all
+  # with -d: same as --no-dereference (and --preserve=links)
+  # and --no-dereference: never follow symbolic links in SOURCE
+  # and -R, -r, --recursive: copy directories recursively
+  # --keep-directory-symlink: if the destination already exists and is a
+  #   symbolic link to a directory, follow the symlink and copy into the directory
+  #   it points to, instead of removing the symlink and creating a real directory in its place.
+  cp_flags="-a --keep-directory-symlink"
+else
+  # -L: always follow symbolic links in SOURCE
+  cp_flags="-Lr --preserve=all --no-preserve=link --keep-directory-symlink"
 fi
 
-# Process multiple input files
-IFS=";" read -ra input_files <<< "$par_input"
-for file in "${input_files[@]}"; do
-  # Check if the file exists before copying
-  if [[ -f "$file" ]]; then
-
-    cp ${extra_params[@]} "$file" "$par_output/"
-    echo "Copied $file to $par_output/"
+# Process multiple input paths (files or directories)
+IFS=";" read -ra input_paths <<< "$par_input"
+for path in "${input_paths[@]}"; do
+  if [[ -e "$path" ]] || [[ -L "$path" ]]; then
+    cp $cp_flags "$path" "$par_output/"
+    echo "Copied $path to $par_output/"
   else
-    echo "Warning: Input file $file does not exist, skipping"
+    echo "Warning: Input path $path does not exist, skipping"
   fi
 done

src/move_files_to_directory/test.sh

@@ -11,7 +11,7 @@ trap clean_up EXIT
 touch "$TMPDIR/test_file.txt"
 touch "$TMPDIR/another_file.txt"
 
-./move_files_to_directory \
+$meta_executable \
   --input "$TMPDIR/test_file.txt" \
   --input "$TMPDIR/another_file.txt" \
   --output "$TMPDIR/test_output"
@@ -19,9 +19,23 @@ touch "$TMPDIR/another_file.txt"
 [[ ! -d "$TMPDIR/test_output" ]] && echo "It seems no output directory is generated" && exit 1
 [[ ! -f "$TMPDIR/test_output/test_file.txt" ]] && [[ ! -f test_output/another_file.txt ]] && echo "Output files were not copied to the output directory" && exit 1
 
+# Test copying a directory
+mkdir -p "$TMPDIR/test_dir"
+touch "$TMPDIR/test_dir/file_in_dir.txt"
+touch "$TMPDIR/test_dir/another_file_in_dir.txt"
+
+$meta_executable \
+  --input "$TMPDIR/test_dir" \
+  --output "$TMPDIR/test_output_dir"
+
+[[ ! -d "$TMPDIR/test_output_dir" ]] && echo "It seems no output directory (test_output_dir) is generated" && exit 1
+[[ ! -d "$TMPDIR/test_output_dir/test_dir" ]] && echo "Input directory was not copied to the output directory" && exit 1
+[[ ! -f "$TMPDIR/test_output_dir/test_dir/file_in_dir.txt" ]] && echo "Files inside the copied directory are missing" && exit 1
+[[ ! -f "$TMPDIR/test_output_dir/test_dir/another_file_in_dir.txt" ]] && echo "Files inside the copied directory are missing" && exit 1
+
 ln -s "$TMPDIR/test_file.txt" "$TMPDIR/symlink.txt"
 
-./move_files_to_directory \
+$meta_executable \
   --input "$TMPDIR/symlink.txt" \
   --output "$TMPDIR/test_output_symlink" \
   --keep_symbolic_links