updated ucftar bash scripts

bash/ucftar_aux_pack

@@ -0,0 +1,152 @@
+#!/bin/bash
+display_help() {
+    (>&2 echo "Usage: $(basename "$0") [-chqv] [-o outfile] indir iseq")
+    (>&2 echo "UCF tar auxiliary packer")
+    (>&2 echo)
+    (>&2 echo "   indir                   path to input directory")
+    (>&2 echo "   iseq                    sequence number with leading zeros")
+    (>&2 echo "   -c, --checksum          compares checksums after the archive is created")
+    (>&2 echo "   -h, --help              display this help message")
+    (>&2 echo "   -o, --outfile           output file (default: snapshot_XXXX.ucf.tar)")
+    (>&2 echo "   -q, --quicksum          same as --checksum, but compares only first bytes")
+    (>&2 echo "   -v, --verbose           verbose output")
+}
+exit_script() {
+    #trap - SIGINT SIGTERM  # clear the trap
+    #kill -- -$$            # Sends SIGTERM to child/sub processes
+    (>&2 echo "SIGINT/SIGTERM received: removing archive")
+    rm $fout
+}
+# Parse command line arguments
+if [ $# -eq 0 ]; then
+  display_help
+  exit -1
+fi
+fout=""
+verbose=0
+checksum=0
+quicksum=0
+POSITIONAL=()
+while [[ $# -gt 0 ]]
+do
+key="$1"
+case $key in
+    -h|--help)
+    display_help
+    exit 0
+    shift # past argument
+    ;;
+    -o|--outfile)
+    fout="$2"
+    shift # past argument
+    shift # past value
+    ;;
+    -v|--verbose)
+    verbose=1
+    shift # past argument
+    ;;
+    -c|--checksum)
+    checksum=1
+    shift # past argument
+    ;;
+    -q|--quicksum)
+    quicksum=1
+    shift # past argument
+    ;;
+    *)    # unknown option
+    POSITIONAL+=("$1") # save it in an array for later
+    shift # past argument
+    ;;
+esac
+done
+set -- "${POSITIONAL[@]}"
+
+# Parse input filename
+din=$1
+seqnum=$2 
+
+# Construct output filename if not specified
+if [ -z "$fout" ]; then
+  fout="auxiliary_${seqnum}.ucf.tar"
+fi
+
+# Display verbose info
+if [ $verbose -eq 1 ]; then
+  (>&2 echo "Creating archive: $fout")
+fi
+
+# Get input files: 
+# following files must exist:
+#   parameters, grid, proc
+# glob auxiliary files:
+#   every file which matches "*_${seqnum}.*", except uvwp, scal, particles
+fparam="parameters_${seqnum}.asc"
+fgrid="grid_${seqnum}.bin"
+fproc="proc_${seqnum}.bin"
+
+#GLOBIGNORE="${din}/parameters_*:${din}/grid_*:${din}/proc_*:${din}/uvwp_*:${din}/scal_*:${din}/particles_*"
+#faux=( $(basename $din/*_${seqnum}.*) )
+#unset GLOBIGNORE
+faux=( $(find ${din} -name "*_${seqnum}.*" ! -name "parameters_*" ! -name "grid_*" ! -name "proc_*" ! -name "particles_*" ! -name "uvwp_*" ! -name "scal_*" -exec basename {} \;) )
+
+# Check if obligatory files are present
+if [ ! -s ${din}/${fparam} ]; then
+  (>&2 echo "[Error] File not found or empty: ${din}/${fparam}")
+  exit 1
+fi
+if [ ! -s ${din}/${fgrid} ]; then
+  (>&2 echo "[Error] File not found or empty: ${din}/${fgrid}")
+  exit 1
+fi
+if [ ! -s ${din}/${fproc} ]; then
+  (>&2 echo "[Error] File not found or empty: ${din}/${fproc}")
+  exit 1
+fi
+
+# Create a full file list for the archive
+flist=(${fparam} ${fgrid} ${fproc} ${faux[@]})
+
+# Now tar them and remove seqence number from file names while doing so
+flagtar=""
+if [ $verbose -eq 1 ]; then
+  flagtar="$flagtar --verbose"
+fi
+trap exit_script SIGINT SIGTERM
+tar $flagtar --format ustar --transform="flags=r;s|_$seqnum||" --directory=${din} -cf ${fout} ${flist[@]}
+tarexit=$?
+# Set exit status accoring to tar
+if [ $tarexit -ne 0 ]; then
+  (>&2 echo "tar failed with exit code $tarexit")
+  exit 254
+fi
+
+# Compare checksums (CNC32), if flag is set
+#din="./archive/" #for testing
+flistx=($(echo ${flist[@]} | sed s/"_$seqnum"/""/g))
+if [ $checksum -eq 1 ]; then
+  for ii in "${!flistx[@]}"; do 
+    if [ $verbose -eq 1 ]; then
+      (>&2 echo "Verifying checksum: ${flist[$ii]}")
+    fi
+    crcori=$(cksum ${din}/${flist[$ii]} | awk '{ print $1, $2 }')
+    crctar=$(tar --to-command='cksum -' -xf ${fout} ${flistx[$ii]} | awk '{ print $1, $2 }')
+    if [ "$crcori" != "$crctar" ]; then
+      (>&2 echo "Verification failed: ${flist[$ii]} ${flistx[$ii]}")
+      exit 5
+    fi
+  done
+elif [ $quicksum -eq 1 ]; then
+  for ii in "${!flistx[@]}"; do
+    if [ $verbose -eq 1 ]; then
+      (>&2 echo "Verifying partial checksum: ${flist[$ii]}")
+    fi
+    crcori=$(head -c 1M ${din}/${flist[$ii]} | cksum -)
+    crctar=$(tar --to-command='head -c 1M' -xf ${fout} ${flistx[$ii]} | cksum -)
+    if [ "$crcori" != "$crctar" ]; then
+      (>&2 echo "Verification failed: ${flist[$ii]} ${flistx[$ii]}")
+      exit 5
+    fi
+  done
+fi
+
+exit 0

bash/ucftar_pack

@@ -4,7 +4,7 @@ display_help() {
     (>&2 echo "UCF tar packer")
     (>&2 echo)
     (>&2 echo "   indir                   path to input directory")
-    (>&2 echo "   iseq                    sequence number")
+    (>&2 echo "   iseq                    sequence number with leading zeros")
     (>&2 echo "   -c, --checksum          compares checksums after the archive is created")
     (>&2 echo "   -h, --help              display this help message")
     (>&2 echo "   -o, --outfile           output file (default: snapshot_XXXX.ucf.tar)")
@@ -63,11 +63,11 @@ set -- "${POSITIONAL[@]}"
 
 # Parse input filename
 din=$1
-seqnum=$(printf %04d $2) 
+seqnum=$2 
 
 # Construct output filename if not specified
 if [ -z "$fout" ]; then
-  fout="snapshot${seqnum}.ucf.tar"
+  fout="snapshot_${seqnum}.ucf.tar"
 fi
 
 # Display verbose info