beefind: rewrote beefind in bash

this should fix issue #48

Makefile

@@ -54,7 +54,7 @@ sed-compat-bashlt4 = -e 'sx\$${\([a-zA-Z_]*\),,}x\$$(tr A-Z a-z <<<\$${\1})xg' \
 
 
 PROGRAMS_C=beeversion beesep beecut beeuniq beesort beegetopt
-PROGRAMS_SHELL=bee beesh
+PROGRAMS_SHELL=bee beesh beefind
 PROGRAMS_PERL=beefind.pl
 
 HELPER_BEE_SHELL=bee-init bee-check bee-remove bee-install bee-list bee-query bee-download bee-update

src/beefind.sh.in

@@ -0,0 +1,269 @@
+#!/bin/bash
+#
+# beefind - scan directory and print files and metadata
+#
+# Copyright (C) 2009-2012
+#       Tobias Dreyer <dreyer@molgen.mpg.de>
+#       Marius Tolzmann <tolzmann@molgen.mpg.de>
+#       and other bee developers
+#
+# This file is part of bee.
+#
+# bee is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+BEE_VERSION="@BEE_VERSION@"
+
+: ${BEE_LIBEXECDIR:=@LIBEXECDIR@}
+: ${BEE_BINDIR:=@BINDIR@}
+
+. ${BEE_LIBEXECDIR}/bee/beelib.config.sh
+
+: ${BEEVERSION:=${BEE_BINDIR}/beeversion}
+: ${BEESEP=${BEE_BINDIR}/beesep}
+
+function usage() {
+    cat <<-EOF
+	beefind v${BEE_VERSION} 2009-2012
+	  by Tobias Dreyer and Marius Tolzmann <{dreyer,tolzmann}@molgen.mpg.de>
+	     Max Planck Institute for Molecular Genetics Berlin Dahlem
+
+	Usage: beefind [options] <files>
+
+	Options:
+	    -c | --cutroot <path>     strip <path> from displayed files
+	    -e | --exclude <pattern>  ignore files matching <pattern>
+	    -s | --skiplist <file>    ignore files matching pattern described in <file>
+
+	    -o | --output <file>      output is redirected into <file> instead of <stdout>
+	    -d | --dump-files <file>  read <file> and just display files; <file> must contain
+	                              beefind output
+
+	    -h | --help               display this help
+
+	EOF
+}
+
+function dump_files() {
+    local infile=${1}
+
+    if [ ! -r "${infile}" ] ; then
+        print_warning "cannot read file '${infile}'"
+        exit 1
+    fi
+
+    for line in $(cat ${infile}) ; do
+        eval $(${BEESEP} ${line})
+
+        echo ${file%//*}
+    done
+}
+
+function get_md5() {
+    local file=${1}
+
+    if [ -L "${file}" ] ; then
+        md5='link'
+    elif [ -d "${file}" ] ; then
+        md5='directory'
+    elif [ -f "${file}" ] ; then
+        md5=$(md5sum ${file})
+        md5=${md5%% *}
+        if [ "$?" != 0 -o -z "${md5}" ] ; then
+            print_warning "failed to create md5 sum for ${file}"
+            md5='#MD5ERROR#'
+        fi
+    elif [ -p "${file}" ] ; then
+        md5='pipe'
+    elif [ -S "${file}" ] ; then
+        md5='socket'
+    elif [ -b "${file}" ] ; then
+        md5='block'
+    elif [ -c "${file}" ] ; then
+        md5='char'
+    elif [ -S "${file}" ] ; then
+        md5='socket'
+    else
+        md5='#MD5UNKNOWN#'
+    fi
+
+    echo ${md5}
+}
+
+function bee_find() {
+    local options=$(${BEE_BINDIR}/beegetopt --name beefind \
+                        --option exclude/e= \
+                        --option skiplist/s= \
+                        -- "${@}")
+
+    if [ $? != 0 ] ; then
+        usage
+        exit 1
+    fi
+
+    eval set -- "${options}"
+
+    declare -a OPT_EXCLUDE
+    declare -a OPT_SKIPLSIT
+
+    while true ; do
+        case "${1}" in
+            --exclude)
+                OPT_EXCLUDE=( ${OPT_EXCLUDE:+${OPT_EXCLUDE[@]}} "${2}" )
+                shift 2
+                ;;
+            --skiplist)
+                OPT_SKIPLIST=( ${OPT_SKIPLIST:+${OPT_SKIPLIST[@]}} "${2}" )
+                shift 2
+                ;;
+            --)
+                shift
+                break
+                ;;
+        esac
+    done
+
+    if [ -z "${1}" ] ; then
+        print_warning "no directory to scan specified"
+        exit 1
+    fi
+
+    find ${1} -mindepth 1 | \
+        grep \
+            --extended-regexp \
+            --invert-match \
+            --file=<(if [ "${#OPT_SKIPLIST[@]}" -gt 0 ] ; then
+                         grep --invert-match --regexp="^ *$" ${OPT_SKIPLIST[@]}
+                     fi) \
+            --file=<(for p in ${OPT_EXCLUDE[@]} ; do
+                         echo ${p}
+                     done)
+}
+
+function do_beefind() {
+    local options=$(${BEE_BINDIR}/beegetopt --name beefind \
+                        --option cutroot/c= \
+                        -- "${@}")
+
+    if [ $? != 0 ] ; then
+        usage
+        exit 1
+    fi
+
+    eval set -- "${options}"
+
+    declare OPT_CUTROOT=
+
+    while true ; do
+        case "${1}" in
+            --cutroot)
+                OPT_CUTROOT="${2}"
+                shift 2
+                ;;
+            --)
+                shift
+                break
+                ;;
+        esac
+    done
+
+    for f in $(cat <(bee_find ${@})) ; do
+        md5=$(get_md5 ${f})
+
+        data=( $(stat -c "%05a %h %u %g %s %Y" ${f}) )
+        if [ "$?" != 0 -o -z "${data}" ] ; then
+            print_warning "can't stat ${f}"
+            exit 1
+        fi
+
+        echo -n "md5=${md5}:"
+        echo -n "omode=${data[0]}:"
+        echo -n "nlink=${data[1]}:"
+        echo -n "uid=${data[2]}:"
+        echo -n "gid=${data[3]}:"
+        echo -n "size=${data[4]}:"
+        echo -n "mtime=${data[5]}:"
+
+        filename=${f}
+        if [ -n "${OPT_CUTROOT}" ] ; then
+            filename=${f#${OPT_CUTROOT}}
+        fi
+        echo -n "file=${filename}"
+
+        if [ "${md5}" = "link" ] ; then
+            echo -n "//$(readlink ${f})"
+        fi
+
+        echo ""
+    done
+}
+
+###############################################################################
+###############################################################################
+###############################################################################
+
+options=$(${BEE_BINDIR}/beegetopt --name beefind \
+                 --option output/o= \
+                 --option dump-files/d= \
+                 --option help/h \
+                 -- "${@}")
+
+if [ $? != 0 ] ; then
+    usage
+    exit 1
+fi
+
+eval set -- "${options}"
+
+declare OPT_OUTPUT=
+declare OPT_DUMPFILES=
+
+while true ; do
+    case "${1}" in
+        --output)
+            OPT_OUTPUT="${2}"
+            shift 2
+            ;;
+        --dump-files)
+            OPT_DUMPFILES="${2}"
+            shift 2
+            ;;
+        --help)
+            usage
+            exit 0
+            ;;
+        --)
+            shift
+            break
+            ;;
+    esac
+done
+
+if [ -n "${OPT_OUTPUT}" ] ; then
+    if ! exec 1>${OPT_OUTPUT} ; then
+        print_warning "can't write to ${OPT_OUTPUT}"
+        exit 1
+    fi
+fi
+
+if [ -n "${OPT_DUMPFILES}" ] ; then
+    if [ ! -r "${OPT_DUMPFILES}" ] ; then
+        print_warning "cannot read file '${OPT_DUMPFILES}'"
+        exit 1
+    fi
+
+    dump_files ${OPT_DUMPFILES}
+    exit 0
+fi
+
+do_beefind ${@}