fix to run Depo script

removing three scripts and putting them into the ews-utils package for storage

scripts/catchup_day.sh

-#/bin/bash
-# A script that runs all of a day's wheat rust forecasts in order
-# 1: depo
-# 2: env
-# 3: epi
-# 4: advisory
-
-echo "starting catchup"
-
-config=$1 # /storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json
-date=$2 # 20221009
-
-# depo
-/storage/app/EWS_prod/code/coordinator/scripts/run_Processor.sh -p Deposition -c $config -s $date --clearup  &
-
-# Wait at least a minute so that logfile timestamps do not clash
-sleep 70
-
-# env
-/storage/app/EWS_prod/code/coordinator/scripts/run_Processor.sh -p Environment -c $config -s $date --clearup &
-
-# wait for depo and env to finish
-wait
-
-# epi
-/storage/app/EWS_prod/code/coordinator/scripts/run_Processor.sh -p Epidemiology -c $config -s $date --clearup &
-
-# Wait at least a minute so that logfile timestamps do not clash
-sleep 70
-
-# advisory
-/storage/app/EWS_prod/code/coordinator/scripts/run_Processor.sh -p Advisory -c $config -s $date --clearup &
-
-wait
-
-echo "finished catchup"

scripts/run_Depo_Processor.sh

 
-source ./run_utils.sh
+# get path of this script (to point to files within the same git repo)
+proc_path="$(dirname "$(readlink -f "$0")")"
+
+source "${proc_path}"/run_utils.sh
 
 setup_conda_env
 
-# get path of this script (to point to files within the same git repo)
-proc_path="$(dirname "$(readlink -f "$0")")"
 
 # run the processor with all arguments
-processor=${proc_path}/../coordinator/ProcessorDeposition.py
-printf "processor is %s\n\n" "$processor"
-python "${processor}" "$@"
+python "${proc_path}"/../coordinator/ProcessorDeposition.py "$@"
 exit_code=$?
 
 teardown_conda_env

scripts/run_EnvPostProcess.sh

-#!/bin/bash
-set -e
-
-# provide custom python packages so they can be imported
-
-# activate conda environment of python modules so they can be imported
-source /storage/app/miniconda3/bin/activate /storage/app/EWS/General/EWS-python/py3EWSepi
-
-python /storage/app/EWS/General/EWS-Coordinator/ENVDataPostProcessor.py "$@"
-
-# deactivate conda environment
-source /storage/app/miniconda3/bin/deactivate /storage/app/EWS/General/EWS-python/py3EWSepi
-

scripts/slice_tar_file_to_bounds.sh

-#!bin/bash
-#slice_tar_file_to_bounds.sh
-echo "CAUTION: Bounds are currently hard-wired"
-echo "It can be calculated automatically, but requires both ogrinfo and cdo to be available"
-
-# activate conda env which has cdo
-# CAUTION: Does not contain rasterio or geopandas, so ogrinfo is not available
-echo "run conda activate conda activate /storage/home/tm689/miniconda3/envs/ewses_env"
-
-tar_file=$1 #/.tar.gz file from Met Office
-bounds_file=$2 # shpfile
-outputdir=$3
-# TODO: Determine lonres and latres in the script
-lonres=0.140625 # can be obtained from any nc in tar file
-latres=0.09375 # can be obtained from any nc in tar file
-
-# 1) Determine bounds of sub-region
-
-bounds_str=$(ogrinfo -so -al $bounds_file | grep "Extent");
-echo "bounds_str: $bounds_str"
-
-coords=($(echo $bounds_str | grep -o -E '[0-9\.]+'));
-
-# bounds of input file
-blonmin=${coords[0]};
-blatmin=${coords[1]};
-blonmax=${coords[2]};
-blatmax=${coords[3];}
-
-# we need nc files to go beyond those bounds by at least one datapoint
-lonmin=$(bc -l <<< "$blonmin - $lonres");
-latmin=$(bc -l <<< "$blatmin - $latres");
-lonmax=$(bc -l <<< "$blonmax + $lonres");
-latmax=$(bc -l <<< "$blatmax + $latres");
-# Hard-wired: Pre-determined for example Ethiopia region
-lonmin=38.60
-lonmax=40.43
-latmin=8.10
-latmax=8.86
-echo "Bounds are $lonmin, $latmin, $lonmax, $latmax"
-
-# 2) get original netcdf files from input tar file
-
-originaldir=$outputdir/original;
-mkdir $originaldir;
-
-tar -zxvf $tar_file -C $originaldir;
-
-# 3) Slice the original netcdf files
-
-# define the output directory
-# remove suffix
-tar_fn=$(basename $tar_file);
-tar_fn_small=${tar_fn%.tar.gz}_small;
-
-outputdir_tar_contents=${outputdir}/${tar_fn_small}/;
-mkdir $outputdir_tar_contents;
-
-nc_fns=$(find $originaldir -type f -name "*.nc");
-
-for fn in $nc_fns; do
-
-    fn_small=${outputdir_tar_contents}$(basename ${fn%.nc})_small.nc;
-
-    echo "cdo command: sellonlatbox,$lonmin,$lonmax,$latmin,$latmax $fn $fn_small";
-    cdo "sellonlatbox,$lonmin,$lonmax,$latmin,$latmax" $fn $fn_small;
-
-done;
-
-# copy over any other files that need to be retained
-fns_to_keep=$(find $originaldir -type f -name "sources.txt");
-cp $fns_to_keep $outputdir_tar_contents;
-
-# 4) Make the smaller tar file
-
-out_fn=$tar_fn_small.tar.gz;
-cd $outputdir;
-tar -zcvf $out_fn ${tar_fn_small}/;
-cd -;
-
-echo "created ${out_fn}";
-
-# clean up 
-
-rm -rf $originaldir;
-rm -rf $outputdir_tar_contents;
-
-echo finished;
-exit 0;
\ No newline at end of file