Ticket #670: eccodes_patch

#!/bin/sh

# INSTRUCTIONS: This patch is intended to be used prior to compiling ecCodes. It
# reduces the severity error/warning  when ecCodes encodes a missing data value
# to a BUFR file, otherwise an overwhelming number of warnings are output.
# Within the ropp2bufr_eccodes and eum2bufr_eccodes tools,
# ECCODES_BUFR_SET_TO_MISSING_IF_OUT_OF_RANGE is set to 1 to make sure
# that a missing data value is set in out-of-range cases.  If the ecCodes BUFR
# library is to be used to write missing data to BUFR files by other means than
# these tools, then this environment variable must be set to 1 manually.
#
# Users should provide the location of their unzipped ecCodes source,
# 'eccodes_path', as a command line argument.  If this is not set, the default
# location in $ROPP_SRC will be used instead.

# Location of un-tar'd eccodes source
eccodes_path=${1:-$ROPP_SRC/eccodes-2.12.5-Source/}
echo 'Using ecCodes path: '$eccodes_path
# Quit if can't find eccodes_path
if [[ ! -d "$eccodes_path" ]] ; then echo "ecCodes path '$eccodes_path' doesn't exist, please fix." ; exit ; fi

# Check if version 2.16 or newer
cd $eccodes_path
package=eccodes-2
for d in $(ls -d $eccodes_path/../$package*); do
  thisdir=${d%%/}               # save this directory/name
  d=$(basename $d); d=${d#$1}   # remove <path><pack> parts
  v=$(expr index $d - 2>/dev/null)      # remove anything else before first '-'...
  if [[ v -le 0 ]]; then
    v=$(expr index $d _ 2>/dev/null)    # ... or '_' if no '-'
  fi
  if [[ v -gt 0 ]]; then
    thisver=${d:$v}                     # what's left is <vers>
  else
    thisver="0"  # assume files with no detectable version are 'v0'
  fi
  if [[ -z "$latestver" ]]; then        # initialise with first file found
    latestdir=$thisdir
    latestver=$thisver
  fi
  if [[ $thisver > $latestver ]]; then  # update if higher <vers>
    latestdir=$thisdir
    latestver=$thisver
    echo 'latestver: '$latestver
  fi
done

if [[ $latestver > 2.16 ]]
then
  version_2_16_onwards=true
else
  version_2_16_onwards=false
fi
echo '####### version_2_16_onwards: '$version_2_16_onwards

# Check the file is there:
if [ ! -f $eccodes_path/src/grib_accessor_class_bufr_data_array.c ]; then
    echo "File not found, exiting. Make sure eccodes_path is set to top-level of unpacked ecCodes."
    exit 1
fi

# If grep doesn't find 3 instances of the pattern, code may have changed. so don't proceed with the patch
n_instances=$(grep -n "Setting it to missing value" $eccodes_path/src/grib_accessor_class_bufr_data_array.c | wc -l)
if [ $n_instances != 3 ] ; then echo "Wrong number of instances found. Exiting" && exit 2 ; fi

# Get line numbers where we need to edit
first=$(grep -n "Setting it to missing value" $eccodes_path/src/grib_accessor_class_bufr_data_array.c | cut -f1 -d: | head -1 )
second=$(grep -n "Setting it to missing value" $eccodes_path/src/grib_accessor_class_bufr_data_array.c | cut -f1 -d: | head -2 | tail -1)
third=$(grep -n "Setting it to missing value" $eccodes_path/src/grib_accessor_class_bufr_data_array.c | cut -f1 -d: | tail -1 )

first="$(($first-1))"
second="$(($second-1))"
third="$(($third-1))"

# Make a backup of the file we're about to edit
cp $eccodes_path/src/grib_accessor_class_bufr_data_array.c $eccodes_path/src/grib_accessor_class_bufr_data_array.c_backup

# Check that backup is made
if [[ ! -f $eccodes_path/src/grib_accessor_class_bufr_data_array.c_backup ]];  then 
  echo "Back up was not created. Check permissions? Exiting." 
  exit
fi

# Change the error type to GRIB_LOG_DEBUG
if [ "$version_2_16_onwards" = false ]
then
  sed -i "$first"','"$first"'s/GRIB_LOG_ERROR/GRIB_LOG_DEBUG/' $eccodes_path/src/grib_accessor_class_bufr_data_array.c 
  sed -i "$second"','"$second"'s/GRIB_LOG_ERROR/GRIB_LOG_DEBUG/' $eccodes_path/src/grib_accessor_class_bufr_data_array.c 
  sed -i "$third"','"$third"'s/GRIB_LOG_ERROR/GRIB_LOG_DEBUG/' $eccodes_path/src/grib_accessor_class_bufr_data_array.c 
fi
if [ "$version_2_16_onwards" = true ]
then
  sed -i "$first"','"$first"'s/ECCODES WARNING/GRIB_LOG_DEBUG/' $eccodes_path/src/grib_accessor_class_bufr_data_array.c
  sed1_exit_code=$?
  sed -i "$second"','"$second"'s/ECCODES WARNING/GRIB_LOG_DEBUG/' $eccodes_path/src/grib_accessor_class_bufr_data_array.c
  sed2_exit_code=$?
  sed -i "$third"','"$third"'s/ECCODES WARNING/GRIB_LOG_DEBUG/' $eccodes_path/src/grib_accessor_class_bufr_data_array.c
  sed3_exit_code=$?
fi

#grep for GRIB_LOG_DEBUG on the relevant lines to test success
if sed "$first"'q;d' $eccodes_path/src/grib_accessor_class_bufr_data_array.c | grep -q GRIB_LOG_DEBUG $eccodes_path/src/grib_accessor_class_bufr_data_array.c
then 

  if sed "$second"'q;d' $eccodes_path/src/grib_accessor_class_bufr_data_array.c | grep -q GRIB_LOG_DEBUG $eccodes_path/src/grib_accessor_class_bufr_data_array.c
  then 

                if sed "$third"'q;d' $eccodes_path/src/grib_accessor_class_bufr_data_array.c | grep -q GRIB_LOG_DEBUG $eccodes_path/src/grib_accessor_class_bufr_data_array.c
                then 

                        printf '\nSuccess. Look at the difference of grib_accessor_class_bufr_data_array.c
                                    and grib_accessor_class_bufr_data_array.c_backup to make sure 
                                    the patch has been applied correctly. If it looks correct, delete
                                    grib_accessor_class_bufr_data_array.c_backup\n\n'
    fi
  fi

else

   printf '\nThere was a problem applying the patch. Try double checking the eccodes exists 
         and is unpacked at the path you supplied for eccodes_path in this script.\n\n'

fi