moving met-resampling to a seperate git repo

scripts/run_Advisory_Processor.sh

@@ -5,11 +5,11 @@ proc_path="$(dirname "$(readlink -f "$0")")"
 
 source "${proc_path}"/run_utils.sh
 
-setup_conda_env
+setup_virtual_env
 
 python "${proc_path}"/../coordinator/ProcessorAdvisory.py "$@"
 exit_code=$?
 
-teardown_conda_env
+teardown_virtual_env
 
 exit $exit_code

scripts/run_Deposition_Processor.sh

@@ -5,13 +5,13 @@ proc_path="$(dirname "$(readlink -f "$0")")"
 
 source "${proc_path}"/run_utils.sh
 
-setup_conda_env
+setup_virtual_env
 
 echo "Running ProcessorDeposition.py with path: "
 pwd;
 python "${proc_path}"/../coordinator/ProcessorDeposition.py "$@"
 exit_code=$?
 
-teardown_conda_env
+teardown_virtual_env
 
 exit $exit_code

scripts/run_Environment_Processor.sh

@@ -5,11 +5,11 @@ proc_path="$(dirname "$(readlink -f "$0")")"
 
 source "${proc_path}"/run_utils.sh
 
-setup_conda_env
+setup_virtual_env
 
 python "${proc_path}"/../coordinator/ProcessorEnvironment.py "$@"
 exit_code=$?
 
-teardown_conda_env
+teardown_virtual_env
 
 exit $exit_code

scripts/run_Epidemiology_Processor.sh

@@ -5,11 +5,11 @@ proc_path="$(dirname "$(readlink -f "$0")")"
 
 source "${proc_path}"/run_utils.sh
 
-setup_conda_env
+setup_virtual_env
 
 python "${proc_path}"/../coordinator/ProcessorEpidemiology.py "$@"
 exit_code=$?
 
-teardown_conda_env
+teardown_virtual_env
 
 exit $exit_code

scripts/run_MetResample_Processor.sh

-#!/bin/bash
-
-# 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
-
-python "${proc_path}"/../coordinator/extra/ProcessorMetResample.py "$@"
-exit_code=$?
-
-teardown_conda_env
-
-exit $exit_code
+##!/bin/bash
+#
+## get path of this script (to point to files within the same git repo)
+#proc_path="$(dirname "$(readlink -f "$0")")"
+#
+#source "${proc_path}"/run_utils.sh
+#
+#setup_virtual_env
+#
+#python "${proc_path}"/../coordinator/extra/ProcessorMetResample.py "$@"
+#exit_code=$?
+#
+#teardown_virtual_env
+#
+#exit $exit_code

scripts/run_Processor.sh

-#!/bin/bash
-
-original_args=("$@")
-
-SHORT=p:h
-OPTS=$(getopt -a --options $SHORT -- "$@")
-echo $OPTS
-eval set -- "$OPTS"
-
-while :
-do
-  case "$1" in
-    -p )
-      component="$2"
-      shift 2
-      ;;
-    -h | --help)
-      "Runs the appropriate Processor component using the -p flag, all other args are passed through"
-      exit 2
-      ;;
-    --)
-      shift;
-      break
-      ;;
-    *)
-      echo "Unexpected option: $1"
-      ;;
-  esac
-done
-
-printf "component is %s" "$component"
-
-if [ "$component" = "Environment" ]; then
-    processor_class="ProcessorEnvironment.py"
-elif [ "$component" = "Deposition" ];then
-    processor_class="ProcessorDeposition.py"
-elif [ "$component" = "Survey" ];then
-    processor_class="ProcessorSurveys.py"
-elif [ "$component" = "Advisory" ];then
-    processor_class="ProcessorAdvisory.py"
-elif [ "$component" = "Scraper" ];then
-    processor_class="ProcessorScraper.py"
-elif [ "$component" = "Epidemiology" ];then
-    processor_class="ProcessorEpidemiology.py"
-else
-    printf "component '%s' not recognised" "$component"
-fi
-
-
-# directory containing all environment
-envs=/storage/app/EWS_prod/envs
-
-# directory containing all custom python packages
-bin=/storage/app/EWS_prod/code/
-
-# provide custom python packages so they can be imported
-flagdir=${bin}/flagdir/
-epimodel=${bin}/epimodel/
-advisory=${bin}/advisory_builder/
-met_processing=${bin}/met_extractor_v2/
-met_processor=${bin}/environmental_suitability/
-plotting=${bin}/plotting/
-post_processing=${bin}/post_processing/
-source_gen=${bin}/source_gen/
-
-export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing
-
-# provide path to email credentials for logging
-
-export EMAIL_CRED=${envs}/credentials/Cred_gmail.json
-
-# activate conda environment of python modules so they can be imported
-#TODO: Move conda_env from bin to envs
-conda_env=${envs}/conda/py3EWS
-source /storage/app/miniconda3/bin/activate ${conda_env}
-
-# get path of this script (to point to files within the same git repo)
-proc_path="$( dirname "$(readlink -f "$0" )" )"
-
-# run the processor with all arguments
-processor=${proc_path}/../coordinator/${processor_class}
-printf "processor is %s\n\n" "$processor"
-python  "${processor}" "${original_args[@]}"
-exit_code=$?;
-
-# deactivate conda environment
-source /storage/app/miniconda3/bin/deactivate ${conda_env}
-
-exit $exit_code;
+#REDUNDANT NOW WE CALL PROCESSOR-SPECIFIC SCRIPTS TO RUN PROCESSORS
+
+##!/bin/bash
+#
+#original_args=("$@")
+#
+#SHORT=p:h
+#OPTS=$(getopt -a --options $SHORT -- "$@")
+#echo $OPTS
+#eval set -- "$OPTS"
+#
+#while :
+#do
+#  case "$1" in
+#    -p )
+#      component="$2"
+#      shift 2
+#      ;;
+#    -h | --help)
+#      "Runs the appropriate Processor component using the -p flag, all other args are passed through"
+#      exit 2
+#      ;;
+#    --)
+#      shift;
+#      break
+#      ;;
+#    *)
+#      echo "Unexpected option: $1"
+#      ;;
+#  esac
+#done
+#
+#printf "component is %s" "$component"
+#
+#if [ "$component" = "Environment" ]; then
+#    processor_class="ProcessorEnvironment.py"
+#elif [ "$component" = "Deposition" ];then
+#    processor_class="ProcessorDeposition.py"
+#elif [ "$component" = "Survey" ];then
+#    processor_class="ProcessorSurveys.py"
+#elif [ "$component" = "Advisory" ];then
+#    processor_class="ProcessorAdvisory.py"
+#elif [ "$component" = "Scraper" ];then
+#    processor_class="ProcessorScraper.py"
+#elif [ "$component" = "Epidemiology" ];then
+#    processor_class="ProcessorEpidemiology.py"
+#else
+#    printf "component '%s' not recognised" "$component"
+#fi
+#
+#
+## directory containing all environment
+#envs=/storage/app/EWS_prod/envs
+#
+## directory containing all custom python packages
+#bin=/storage/app/EWS_prod/code/
+#
+## provide custom python packages so they can be imported
+#flagdir=${bin}/flagdir/
+#epimodel=${bin}/epimodel/
+#advisory=${bin}/advisory_builder/
+#met_processing=${bin}/met_extractor_v2/
+#met_processor=${bin}/environmental_suitability/
+#plotting=${bin}/plotting/
+#post_processing=${bin}/post_processing/
+#source_gen=${bin}/source_gen/
+#
+#export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing
+#
+## provide path to email credentials for logging
+#
+#export EMAIL_CRED=${envs}/credentials/Cred_gmail.json
+#
+## activate conda environment of python modules so they can be imported
+##TODO: Move conda_env from bin to envs
+#conda_env=${envs}/conda/py3EWS
+#source /storage/app/miniconda3/bin/activate ${conda_env}
+#
+## get path of this script (to point to files within the same git repo)
+#proc_path="$( dirname "$(readlink -f "$0" )" )"
+#
+## run the processor with all arguments
+#processor=${proc_path}/../coordinator/${processor_class}
+#printf "processor is %s\n\n" "$processor"
+#python  "${processor}" "${original_args[@]}"
+#exit_code=$?;
+#
+## deactivate conda environment
+#source /storage/app/miniconda3/bin/deactivate ${conda_env}
+#
+#exit $exit_code;

scripts/run_Scraper_Processor.sh

@@ -5,11 +5,11 @@ proc_path="$(dirname "$(readlink -f "$0")")"
 
 source "${proc_path}"/run_utils.sh
 
-setup_conda_env
+setup_virtual_env
 
 python "${proc_path}"/../coordinator/ProcessorScraper.py "$@"
 exit_code=$?
 
-teardown_conda_env
+teardown_virtual_env
 
 exit $exit_code

scripts/run_Survey_Processor.sh

@@ -5,11 +5,11 @@ proc_path="$(dirname "$(readlink -f "$0")")"
 
 source "${proc_path}"/run_utils.sh
 
-setup_conda_env
+setup_virtual_env
 
 python "${proc_path}"/../coordinator/ProcessorSurveys.py "$@"
 exit_code=$?
 
-teardown_conda_env
+teardown_virtual_env
 
 exit $exit_code

scripts/run_utils.sh

 #!/bin/bash
 
-function setup_conda_env() {
+function setup_virtual_env() {
   # directory containing all environment
   envs=/storage/app/EWS_prod/envs
 
@@ -30,9 +30,8 @@ function setup_conda_env() {
   source ${venv}/ews_prod/bin/activate;
 }
 
-function teardown_conda_env() {
+function teardown_virtual_env() {
   # deactivate conda environment
   deactivate;
-
 }