78 lines
1.6 KiB
Bash
Executable File
78 lines
1.6 KiB
Bash
Executable File
#!/bin/bash
|
|
|
|
run_pipeline() {
|
|
if [ $TYPE == 'frequency' ]
|
|
then
|
|
CONFIG_FILE="./tests/settings/frequency_config.yaml"
|
|
else
|
|
CONFIG_FILE="./tests/settings/periodic_config.yaml"
|
|
fi
|
|
|
|
echo "Copying participant files"
|
|
cp -r tests/data/external/participant_files/* data/external/participant_files/
|
|
|
|
echo $TYPE
|
|
echo "Deleting old outputs"
|
|
snakemake --configfile=$(echo $CONFIG_FILE) --delete-all-output -j1
|
|
|
|
echo "Running RAPIDS"
|
|
snakemake --configfile=$(echo $CONFIG_FILE) -R pull_phone_data -j1
|
|
}
|
|
|
|
display_usage() {
|
|
echo "Usage: run_test.sh [-t|--type] [periodic | frequency] [-a|--action] [ all | run | test]"
|
|
exit 1
|
|
}
|
|
|
|
POSITIONAL=()
|
|
while [[ $# -gt 0 ]]
|
|
do
|
|
key="$1"
|
|
|
|
case $key in
|
|
-t|--type)
|
|
TYPE="$2"
|
|
shift # past argument
|
|
shift # past value
|
|
;;
|
|
-a|--action)
|
|
ACTION="$2"
|
|
shift # past argument
|
|
shift # past value
|
|
;;
|
|
*) # unknown option
|
|
POSITIONAL+=("$1") # save it in an array for later
|
|
shift # past argument
|
|
;;
|
|
esac
|
|
done
|
|
|
|
if [ $ACTION != 'test' ] && [ $ACTION != 'run' ] && [ $ACTION != 'both' ]
|
|
then
|
|
display_usage
|
|
fi
|
|
|
|
if [[ $TYPE == 'all' ]]
|
|
then
|
|
TYPE="frequency"
|
|
run_pipeline
|
|
python tests/scripts/run_tests.py frequency
|
|
TYPE="periodic"
|
|
run_pipeline
|
|
python tests/scripts/run_tests.py periodic
|
|
else
|
|
if [ $TYPE != 'frequency' ] && [ $TYPE != 'periodic' ]
|
|
then
|
|
display_usage
|
|
fi
|
|
|
|
if { [ $ACTION == 'run' ] || [ $ACTION == 'both' ]; }
|
|
then
|
|
run_pipeline
|
|
fi
|
|
if { [ $ACTION == 'test' ] || [ $ACTION == 'both' ]; }
|
|
then
|
|
python tests/scripts/run_tests.py $(echo $TYPE)
|
|
fi
|
|
fi
|