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"planemo upload commit c2694fb4aa55c4f25eb53db73496eaf5e56d7872"
author prog
date Wed, 08 Jan 2020 12:47:49 +0000
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deb654d58b15 "planemo upload commit c2694fb4aa55c4f25eb53db73496eaf5e56d7872"
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1 #!/bin/bash
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2 # vi: fdm=marker
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3
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4 # Constants {{{1
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5 ################################################################
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6
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7 PROG_NAME=$(basename $0)
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8 PROG_PATH=$(dirname $0)
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9 YES=yes
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10 NO=no
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11
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12 # Global variables {{{1
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13 ################################################################
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14
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15 DEBUG=0
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16 EXT=
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17 INPUT_DIR=
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18 OUTPUT_DIR=
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19 SYMLINK=$NO
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20
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21 # Print help {{{1
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22 ################################################################
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23
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24 function print_help {
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25 echo "Usage: $PROG_NAME -i <ISA_DIR> -e <EXT> -o <OUTPUT_DIR>"
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26 echo
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27 echo "Extract files with a given extension from ISA-Tab archives into a collection."
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28 echo
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29 echo "Options:"
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30 echo " -e, --ext EXT The extension of the files to find."
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31 echo " -h, --help Print this help message."
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32 echo " -i, --input DIR Input directory containing ISA archive."
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33 echo " -o, --output DIR Set the output directory to use."
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34 echo " -s, --symlink Create symbolic links instead of copying files."
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35 }
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36
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37 # Error {{{1
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38 ################################################################
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39
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40 function error {
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41
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42 local msg=$1
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43
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44 echo "ERROR: $msg" >&2
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45
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46 exit 1
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47 }
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48
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49 # Print debug msg {{{1
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50 ################################################################
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51
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52 function print_debug_msg {
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53
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54 local dbglvl=$1
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55 local dbgmsg=$2
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56
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57 [ $DEBUG -ge $dbglvl ] && echo "[DEBUG] $dbgmsg" >&2
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58 }
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59
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60 # Read args {{{1
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61 ################################################################
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62
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63 function read_args {
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64
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65 local args="$*" # save arguments for debugging purpose
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66
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67 # Read options
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68 while true ; do
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69 shift_count=1
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70 case $1 in
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71 -e|--ext) EXT="$2" ; shift_count=2 ;;
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72 -g|--debug) DEBUG=$((DEBUG + 1)) ;;
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73 -h|--help) print_help ; exit 0 ;;
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74 -i|--input) INPUT_DIR="$2" ; shift_count=2 ;;
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75 -o|--output) OUTPUT_DIR="$2" ; shift_count=2 ;;
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76 -s|--symlink) SYMLINK=$YES ;;
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77 -) error "Illegal option $1." ;;
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78 --) error "Illegal option $1." ;;
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79 --*) error "Illegal option $1." ;;
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80 -?) error "Unknown option $1." ;;
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81 -[^-]*) split_opt=$(echo $1 | sed 's/^-//' | sed 's/\([a-zA-Z]\)/ -\1/g') ; set -- $1$split_opt "${@:2}" ;;
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82 *) break
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83 esac
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84 shift $shift_count
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85 done
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86 shift $((OPTIND - 1))
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87
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88 # Debug
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89 print_debug_msg 1 "Arguments are : $args"
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90
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91 # Check input params
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92 [[ $# -eq 0 ]] || error "No remaining arguments are allowed."
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93 [[ -n $INPUT_DIR ]] || error "You must specify an input directory, using -i option."
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94 [[ -d $INPUT_DIR ]] || error "\"$INPUT_DIR\" is not a valid directory."
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95 [[ -n $OUTPUT_DIR ]] || error "You must specify an output directory, using -o option."
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96 [[ ! -e $OUTPUT_DIR ]] || error "\"$OUTPUT_DIR\" already exists."
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97 [[ -n $EXT ]] || error "You must specify the extension of the files you are looking for, with the -e option."
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98 }
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99
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100 # MAIN {{{1
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101 ################################################################
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102
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103 read_args "$@"
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104
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105 # Create output directory
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106 print_debug_msg 1 "Create output directory \"$OUTPUT_DIR\"."
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107 mkdir -p "$OUTPUT_DIR"
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108
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109 # Find files to extract
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110 print_debug_msg 1 "Find \"$EXT\" files to extract in \"$INPUT_DIR\"."
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111 files_to_extract=$(mktemp -t tmp.XXXXXX)
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112 find "$(realpath $INPUT_DIR)" -iname "*.$EXT" >files_to_extract
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113 print_debug_msg 1 "Files to extract:"
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114 if [[ $DEBUG -ge 1 ]] ; then
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115 cat files_to_extract >&2
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116 fi
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117
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118 # Extract files
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119 if [[ $SYMLINK == $YES ]] ; then
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120 print_debug_msg 1 "Create symbolic links of all \"$EXT\" files to extract into \"$OUTPUT_DIR\"."
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121 xargs -I % ln -s % "$OUTPUT_DIR" <files_to_extract
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122 else
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123 print_debug_msg 1 "Copy all \"$EXT\" files to extract to \"$OUTPUT_DIR\"."
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124 xargs -I % cp % "$OUTPUT_DIR" <files_to_extract
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125 fi
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126 rm files_to_extract
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127 print_debug_msg 1 "Files extracted:"
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128 if [[ $DEBUG -ge 1 ]] ; then
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129 ls -1 "$OUTPUT_DIR" >&2
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130 fi