mkprocdata_map_all

#!/bin/bash

# This script runs mkprocdata_map_wrap on all files matching a given
# pattern within a directory.

# Created by Bill Sacks, 5-26-11

# ----------------------------------------------------------------------
# LOCAL FUNCTIONS DEFINED HERE
# ----------------------------------------------------------------------

function Usage {
    script_name=`basename $0`
    echo "Usage: $script_name -p prefix -m map_file -t template_file [-d] [-e executable-path] [-h] [-i] [-l] [-o output_suffix] [-r diRectory] [-s suffix]"
    echo ""
    echo "This script runs mkprocdata_map_wrap on all files matching a"
    echo "given pattern within a directory."
    echo ""
    echo "'prefix' gives the prefix of the files on which"
    echo "mkprocdata_map_wrap should be run; 'prefix' should NOT contain"
    echo "wildcard characters. The prefix is also used to translate"
    echo "from input to output file names (see examples below)"
    echo ""
    echo "'map_file' gives the name (and full path if not in the current"
    echo "directory) of the mapping file"
    echo ""
    echo "'template_file' gives the name (and full path if not in the"
    echo "current directory) of the template file, from which we read"
    echo "lats, lons and some other variables"
    echo ""
    echo "The following are optional arguments:"
    echo ""
    echo "[-d]: Do a test (Dry run): do all error-checking on"
    echo "      arguments and print commands that would be run, but"
    echo "      don't actually run commands"
    echo ""
    echo "[-e executable-path]: Gives the path of the mkprocdata_map executable."
    echo "                      If not specified, the path is determined by the"
    echo "                      default value in mkprocdata_map_wrap."
    echo ""
    echo "[-h]: Print this help message and exit"
    echo ""
    echo "[-i]: Ignore (skip) existing output files; if this option is"
    echo "      not specified, then the script dies with an error if"
    echo "      any of the desired output files already exist"
    echo ""
    echo "[-l]: Option passed to mkprocdata_map_wrap: rather than computing"
    echo "      landfrac and related variables by regridding the input file,"
    echo "      instead copy these variables directly from the template file."
    echo ""
    echo "[-o output_suffix]: suffix to append to the end of the prefix"
    echo "                    on the output files"
    echo "                    If not specified, '_2d' is used"
    echo ""
    echo "[-r diRectory]: Do the processing in the given directory."
    echo "                If not specified, processing is done in the"
    echo "                current working directory."
    echo ""
    echo "[-s suffix]: Run mkprocdata_map_wrap on all files matching the"
    echo "             pattern '\${prefix}\${suffix}'. The suffix can -"
    echo "             and often will - contain wildcards; but"
    echo "             remember to enclose 'suffix' in quotes to"
    echo "             prevent shell expansion."
    echo "             If not specified, run mkprocdata_map_wrap on all"
    echo "             files matching '\${prefix}*'"
    echo ""
    echo ""
    echo "Example: $script_name -p Ib14_ne30np4_gx1v6 -m map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc -t Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc"
    echo "This will run mkprocdata_map_wrap on all files whose names begin"
    echo "with 'Ib14_ne30np4_gx1v6' in the current directory, using the"
    echo "mapping file named 'map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc'"
    echo "and the template file named 'Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc'"
    echo "For an input file named:"
    echo "  Ib14_ne30np4_gx1v6.clm2.h0.0001-01-06-00000.nc"
    echo "The output file will be named:"
    echo "  Ib14_ne30np4_gx1v6_2d.clm2.h0.0001-01-06-00000.nc"
    echo ""
    echo "Example: $script_name -o '_remap' -s '*.h0.0001*.nc' -p Ib14_ne30np4_gx1v6 -m map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc -t Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc"
    echo "This will run mkprocdata_map_wrap on all files whose names match"
    echo "the pattern 'Ib14_ne30np4_gx1v6*.h0.0001*.nc', in the"
    echo "current directory, using the mapping file named"
    echo "'map_ne30np4_to_fv1.9x2.5_aave_da_091230.nc' and the"
    echo "template file named Ib19_1.9x2.5_gx1v6.clm2.h0.0001-01.nc"
    echo "For an input file named:"
    echo "  Ib14_ne30np4_gx1v6.clm2.h0.0001-01-06-00000.nc"
    echo "The output file will be named:"
    echo "  Ib14_ne30np4_gx1v6_remap.clm2.h0.0001-01-06-00000.nc"
    echo ""
}

# ----------------------------------------------------------------------
# BEGIN MAIN SCRIPT
# ----------------------------------------------------------------------

script_dir=`dirname $0`
source $script_dir/mkprocdata_map_functions.bash

# ----------------------------------------------------------------------
# Handle command-line arguments
# ----------------------------------------------------------------------

# define default values:
# required arguments:
prefix=""
map_file=""
template_file=""
# optional arguments:
directory="."
ignore_existing=0
output_suffix="_2d"
suffix="*"
dryrun=0
extra_args=""

while getopts de:hilm:o:p:r:s:t: opt; do
    case $opt in
	d) dryrun=1;;
	e) extra_args="$extra_args -e $OPTARG";;
	h) Usage; exit;;
	i) ignore_existing=1;;
	l) extra_args="$extra_args -l";;
	m) map_file=$OPTARG;;
	o) output_suffix=$OPTARG;;
	p) prefix=$OPTARG;;
	r) directory=$OPTARG;;
	s) suffix=$OPTARG;;
	t) template_file=$OPTARG;;
	\?) Usage; exit 1
    esac
done

# ----------------------------------------------------------------------
# Error checking on arguments
# ----------------------------------------------------------------------

if [ -z "$prefix" ]; then
    echo "Must specify a prefix"
    Usage
    exit 1
fi

check_file_arg "$map_file" "map"
check_file_arg "$template_file" "template"

# Make sure directory is really a directory
if [ ! -d $directory ]; then
    echo "ERROR: $directory is not a directory"
    echo ""
    Usage
    exit 1
fi


# ----------------------------------------------------------------------
# Change to desired directory
# ----------------------------------------------------------------------

olddir=`pwd`
cd $directory

# ----------------------------------------------------------------------
# Get list of files matching the given pattern; make sure there really
# are some matching files
# ----------------------------------------------------------------------

files=`ls ${prefix}${suffix}`
if [ $? -ne 0 ]; then
    echo "ERROR trying to find files matching: ${prefix}${suffix}"
    echo ""
    Usage
    exit 1
fi

# ----------------------------------------------------------------------
# Loop through files matching the given pattern; run mkprocdata_map_wrap for each
# ----------------------------------------------------------------------

for infile in $files; do
    outfile=${infile/$prefix/${prefix}${output_suffix}}
    if [ -e $outfile ]; then
	if [ $ignore_existing -eq 0 ]; then
	    echo ""
	    echo "ERROR: output file $outfile already exists"
	    exit 1
	else
	    echo ""
	    echo "WARNING: output file $outfile already exists: skipping"
	    echo ""
	fi
    
    else  # outfile does not exist
	echo ""
	do_cmd "${script_dir}/mkprocdata_map_wrap -i $infile -o $outfile -m $map_file -t $template_file $extra_args" $dryrun
    fi
done

# ----------------------------------------------------------------------
# Clean up
# ----------------------------------------------------------------------

cd $olddir