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