FEAT: add untar

CHANGELOG

@@ -2,4 +2,7 @@
 
 ## NEW FEATURES
 
-* `csv2fasta`: Convert two columns from a CSV file to FASTA entries (PR #1).
+* `csv2fasta`: Convert two columns from a CSV file to FASTA entries (PR #1).
+
+* `untar`: Unpack a .tar file. When the contents of the .tar file is just a single directory,
+   put the contents of the directory into the output folder instead of that directory (PR #3).

src/untar/config.vsh.yaml

@@ -0,0 +1,43 @@
+name: untar
+description: |
+  Unpack a .tar file. When the contents of the .tar file is just a single directory,
+  put the contents of the directory into the output folder instead of that directory.
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Tarball file to be unpacked.
+        type: file
+        required: true
+  - name: Output arguments
+    arguments:
+      - name: --output
+        description: Directory to write the contents of the .tar file to.
+        type: file
+        direction: output
+        required: true
+  - name: "Other arguments"
+    arguments:
+      - name: "--exclude"
+        alternatives: ["-e"]
+        type: string
+        description: Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted.
+        example: "docs/figures"
+        required: false
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages:
+          - procps
+
+runners:
+  - type: executable
+  - type: nextflow

src/untar/script.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+extra_args=()
+
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Check if tarball contains 1 top-level directory. If so, extract the contents of the
+# directory to the output directory instead of the directory itself.
+echo "Directory contents:"
+tar -taf "${par_input}" > "$TMPDIR/tar_contents.txt"
+cat "$TMPDIR/tar_contents.txt"
+
+printf "Checking if tarball contains only a single top-level directory: "
+if [[ $(grep -o -E '^[./]*[^/]+/$' "$TMPDIR/tar_contents.txt" | uniq | wc -l) -eq 1 ]]; then
+    echo "It does."
+    echo "Extracting the contents of the top-level directory to the output directory instead of the directory itself."
+    # The directory can be both of the format './<directory>' (or ././<directory>) or just <directory>
+    # Adjust the number of stripped components accordingly by looking for './' at the beginning of the file.
+    starting_relative=$(grep -oP -m 1 '^(./)*' "$TMPDIR/tar_contents.txt" | tr -d '\n' | wc -c)
+    n_strips=$(( ($starting_relative / 2)+1 ))
+    extra_args+=("--strip-components=$n_strips")
+else
+    echo "It does not."
+fi
+
+if [ "$par_exclude" != "" ]; then
+    echo "Exclusion of files with wildcard '$par_exclude' requested."
+    extra_args+=("--exclude=$par_exclude")
+fi
+
+echo "Starting extraction of tarball '$par_input' to output directory '$par_output'."
+mkdir -p "$par_output"
+echo "executing 'tar --no-same-owner --no-same-permissions --directory=$par_output ${extra_args[@]} -xavf $par_input'"
+tar --no-same-owner --no-same-permissions --directory="$par_output" ${extra_args[@]} -xavf "$par_input"
+

src/untar/test.sh

@@ -0,0 +1,126 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+# create tempdir
+echo ">>> Creating temporary test directory."
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+echo ">>> Created temporary directory '$TMPDIR'."
+
+INPUT_FILE="$TMPDIR/test_file.txt"
+echo ">>> Creating test input file at '$TMPDIR/test_file.txt'."
+echo "foo" > "$INPUT_FILE"
+echo ">>> Created '$INPUT_FILE'."
+
+echo ">>> Creating tar.gz from '$INPUT_FILE'."
+TARFILE="${INPUT_FILE}.tar.gz"
+tar -C "$TMPDIR" -czvf ${INPUT_FILE}.tar.gz $(basename "$INPUT_FILE")
+[[ ! -f "$TARFILE" ]] && echo ">>> Test setup failed: could not create tarfile." && exit 1
+echo ">>> '$TARFILE' created."
+
+echo ">>> Check whether tar.gz can be extracted"
+echo ">>> Creating temporary output directory for test 1."
+OUTPUT_DIR_1="$TMPDIR/output_test_1/"
+mkdir "$OUTPUT_DIR_1"
+
+echo ">>> Extracting '$TARFILE' to '$OUTPUT_DIR_1'".
+$meta_executable \
+   --input "$TARFILE" \
+   --output "$OUTPUT_DIR_1"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_1/test_file.txt" ]] && echo "Output file could not be found. Output directory contents: " && ls "$OUTPUT_DIR_1" && exit 1
+
+echo ">>> Creating temporary output directory for test 2."
+OUTPUT_DIR_2="$TMPDIR/output_test_2/"
+mkdir "$OUTPUT_DIR_2"
+
+echo ">>> Extracting '$TARFILE' to '$OUTPUT_DIR_2', excluding '$test_file.txt'".
+$meta_executable \
+   --input "$TARFILE" \
+   --output "$OUTPUT_DIR_2" \
+   --exclude 'test_file.txt'
+
+echo ">>> Check whether excluded file was not extracted"
+[[ -f "$OUTPUT_DIR_2/test_file.txt" ]] && echo "File should have been excluded! Output directory contents:" && ls "$OUTPUT_DIR_2" && exit 1
+
+echo ">>> Creating test tarball containing only 1 top-level directory."
+mkdir "$TMPDIR/input_test_3/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_3/"
+tar -C "$TMPDIR" -czvf "$TMPDIR/input_test_3.tar.gz" $(basename "$TMPDIR/input_test_3")
+TARFILE_3="$TMPDIR/input_test_3.tar.gz"
+
+echo ">>> Creating temporary output directory for test 3."
+OUTPUT_DIR_3="$TMPDIR/output_test_3/"
+mkdir "$OUTPUT_DIR_3"
+
+echo "Extracting '$TARFILE_3' to '$OUTPUT_DIR_3'".
+$meta_executable \
+   --input "$TARFILE_3" \
+   --output "$OUTPUT_DIR_3"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_3/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+
+echo ">>> Check for tar archive that contains a single directory starting with './'."
+mkdir "$TMPDIR/input_test_4/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_4/"
+
+pushd "$TMPDIR/" 
+trap popd ERR
+tar -czvf "$TMPDIR/input_test_4.tar.gz" ./input_test_4
+popd
+trap - ERR
+
+OUTPUT_DIR_4="$TMPDIR/output_test_4/"
+echo "Extracting '$TMPDIR/input_test_4.tar.gz' to '$OUTPUT_DIR_4'".
+$meta_executable \
+   --input "$TMPDIR/input_test_4.tar.gz" \
+   --output "$OUTPUT_DIR_4"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_4/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+
+echo ">>> Creating test tarball containing only 1 top-level directory, but it is nested."
+mkdir -p "$TMPDIR/input_test_5/nested/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_5/nested/"
+tar -C "$TMPDIR" -czvf "$TMPDIR/input_test_5.tar.gz" $(basename "$TMPDIR/input_test_5")
+TARFILE_5="$TMPDIR/input_test_5.tar.gz"
+
+echo ">>> Creating temporary output directory for test 5."
+OUTPUT_DIR_5="$TMPDIR/output_test_5/"
+mkdir "$OUTPUT_DIR_5"
+
+echo "Extracting '$TARFILE_5' to '$OUTPUT_DIR_5'".
+$meta_executable \
+   --input "$TARFILE_5" \
+   --output "$OUTPUT_DIR_5"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_5/nested/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+
+echo ">>> Creating test tarball containing two top-level directories."
+mkdir -p "$TMPDIR/input_test_6/number_1/"
+mkdir "$TMPDIR/input_test_6/number_2/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_6/number_1/"
+tar -C "$TMPDIR" -czvf "$TMPDIR/input_test_6.tar.gz" $(basename "$TMPDIR/input_test_6")
+TARFILE_6="$TMPDIR/input_test_6.tar.gz"
+
+echo ">>> Creating temporary output directory for test 6."
+OUTPUT_DIR_6="$TMPDIR/output_test_6/"
+mkdir "$OUTPUT_DIR_6"
+
+echo "Extracting '$TARFILE_6' to '$OUTPUT_DIR_6'".
+$meta_executable \
+   --input "$TARFILE_6" \
+   --output "$OUTPUT_DIR_6"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_6/number_1/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+[[ ! -d "$OUTPUT_DIR_6/number_2" ]] && echo "Output directory could not be found!" && exit 1
+
+echo ">>> Test finished successfully"