From 677dbeb9bfab08b8e19e88153ed7b524d8703108 Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Tue, 20 Feb 2018 17:36:05 +0100
Subject: [PATCH] ENH Add 'mv_keep_parents'
---
README.rst | 2 +
bin/mv_keep_parents | 127 ++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 129 insertions(+)
create mode 100755 bin/mv_keep_parents
diff --git a/README.rst b/README.rst
index 3143042..e15f6ce 100644
--- a/README.rst
+++ b/README.rst
@@ -17,6 +17,8 @@ EMBL utilities
``qs`` - collect queue status across different SGE clusters/queues. Requires key-based authentication with SSH.
+``mv_keep_parents`` - equivalent to ``cp --parents src/*.txt dest/`` but moving instead of copying. Optionally keeping source directories if empty with option ``-k``.
+
Examples
========
diff --git a/bin/mv_keep_parents b/bin/mv_keep_parents
new file mode 100755
index 0000000..82a6f36
--- /dev/null
+++ b/bin/mv_keep_parents
@@ -0,0 +1,127 @@
+#!/usr/bin/env bash
+
+ERROR="[31;1mERROR:[0m"
+KEEPDIRS=0
+VERBOSE=0
+DRYRUN=""
+
+usage() {
+ echo >&2 ""
+ echo >&2 "Usage:"
+ echo >&2 " $0 [-k] source1 [source2 [...]] destination"
+ echo >&2 ""
+ echo >&2 "Will move files from all specified sources to destination"
+ echo >&2 "while preserving the folder structure of each source"
+ echo >&2 ""
+ echo >&2 "Options:"
+ echo >&2 " -k --keepdirs = keep source directories even if empty. Defaults to removing if empty"
+ echo >&2 " -d --dryrun = simulate execution without performing actions on the filesystem"
+ echo >&2 " echoes most actions that would be performed"
+ echo >&2 " removal of empty directories isn't simulated"
+ echo >&2 " -v --verbose = echo verbose info while executing. Defaults to non-verbose execution"
+ echo >&2 ""
+ echo >&2 "Example:"
+ echo >&2 " $0 path/to/*.txt destination -> destination/path/to/*.txt"
+ echo >&2 ""
+}
+
+move_preserve_path() {
+ parent="$(dirname "$1")"
+
+ $DRYRUN mkdir -p "$2/$parent"
+ $DRYRUN mv "$1" "$2/$parent"
+
+ if [ "$3" -eq 0 ]; then
+ empty_dir_remove_recurse "$parent"
+ fi
+}
+
+empty_dir_remove_recurse() {
+ # If the dir to remove is the current, don't even try
+ if [ "$1" == "." ] || [ "$1" == "$(pwd)" ]; then
+ return 0
+ fi
+
+ # Remove original directory if empty (recurses path backwards)
+ if [ -z "$(ls -A "$1")" ]; then
+ $DRYRUN rmdir "$1"
+
+ empty_dir_remove_recurse "$(dirname "$1")"
+ fi
+}
+
+generic_error() {
+ usage
+ echo >&2 "${ERROR} $1"
+ echo >&2 ""
+ exit 1
+}
+
+ARG_PARSE="getopt -o vkdh -l verbose,keepdirs,dryrun,help -n $0 --"
+
+# We process arguments twice to handle any argument parsing error:
+ARG_ERROR=$($ARG_PARSE "$@" 2>&1 1>/dev/null)
+
+if [ $? -ne 0 ]; then
+ generic_error "$ARG_ERROR"
+fi
+
+# Abort on any errors from this point onwards
+set -euo pipefail
+
+# Parse args using getopt (instead of getopts) to allow arguments before options
+ARGS=$($ARG_PARSE "$@")
+
+# reorganize arguments as returned by getopt
+eval set -- "$ARGS"
+
+while true; do
+ case "$1" in
+ # Shift before to throw away option
+ # Shift after if option has a required positional argument
+ -v|--verbose)
+ shift
+ VERBOSE=1
+ ;;
+ -k|--keepdirs)
+ shift
+ KEEPDIRS=1
+ ;;
+ -d|--dryrun)
+ shift
+ DRYRUN="echo"
+ ;;
+ -h|--help)
+ shift
+ usage
+ exit 1
+ ;;
+ --)
+ shift
+ break
+ ;;
+ esac
+done
+
+if [ "$#" -lt 2 ]; then
+ generic_error "$0 requires at least 2 arguments - source and destination"
+fi
+
+# enable verbose execution
+if [ "$VERBOSE" -eq 1 ]; then
+ set -euxo pipefail
+fi
+
+DEST="${!#}"
+
+if [ ! -d "$DEST" ]; then
+ generic_error "Destination $DEST doesn't exist"
+fi
+
+while [ "$#" -ge 2 ]; do
+ SRC="$1"
+ shift
+ move_preserve_path "$SRC" "$DEST" "$KEEPDIRS"
+done
+
+# vim: ai sts=4 et sw=4
--
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