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#!/bin/bash
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# Bash script to create a new postgis database and prep it with GADM
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# data for geovalidation purposes.
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#
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# Basic workflow:
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# 1. Load geoscrub input data into database
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# 2. Scrub geoscrub input data with the geonames.sql script
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# 3. Scrub geoscrub input data with the geovalidate.sql script
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#
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# Paul Sarando
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# iPlant Collaborative
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# Oct 2013
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DB_NAME="geoscrub"
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DB_USER="bien"
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DB_HOST_OPT=""
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SCRIPT_DIR="$(dirname $0)"
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function usage {
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echo "Usage: $0 [OPTIONS]" >&2
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echo "Valid Options:" >&2
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echo "-d, --dbname=DBNAME database name psql commands will connect to" >&2
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echo "-h, --host=HOSTNAME database server host or socket directory" >&2
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echo "-U, --username=USERNAME database user name" >&2
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echo "Geoscrub Data Options:" >&2
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echo "-i, --geoscrub-input Geoscrub input directory (default: ${HOME}/geoscrub_input)" >&2
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echo " Delete this directory, or the input CSV in it," >&2
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echo " to re-download the data." >&2
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echo "-o, --output-file Optional file where geoscrubbed CSV should be saved." >&2
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echo " If this option is given, then the final geoscrub table" >&2
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echo " will be dumped to the specified file in CSV format." >&2
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echo " No output file is saved if this option is omitted." >&2
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exit 1;
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}
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while [[ $# -gt 0 ]]; do
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case "$1" in
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-\? | --help)
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usage
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;;
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-h)
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if [[ -z $2 ]]; then
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echo "Option $1 requires an argument." >&2
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usage
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fi
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DB_HOST_OPT="-h $2"
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shift 2
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;;
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--host=*)
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DB_HOST_OPT="-h ${1#*=}"
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shift
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;;
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-U)
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if [[ -z $2 ]]; then
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echo "Option $1 requires an argument." >&2
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usage
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fi
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DB_USER="$2"
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shift 2
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;;
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--username=*)
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DB_USER="${1#*=}"
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shift
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;;
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-d)
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if [[ -z $2 ]]; then
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echo "Option $1 requires an argument." >&2
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usage
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fi
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DB_NAME="$2"
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shift 2
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;;
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--dbname=*)
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DB_NAME="${1#*=}"
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shift
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;;
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-i)
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if [[ -z $2 ]]; then
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echo "Option $1 requires an argument." >&2
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usage
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fi
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GEOSCRUB_INPUT_OPT="-i $2"
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shift 2
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;;
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--geoscrub-input=*)
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GEOSCRUB_INPUT_OPT="$1"
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shift
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;;
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-o)
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if [[ -z $2 ]]; then
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echo "Option $1 requires an argument." >&2
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exit 1;
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fi
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OUTPUT_FILE="$2"
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shift 2
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;;
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--output-file=*)
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OUTPUT_FILE="${1#*=}"
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shift
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;;
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*)
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echo "Invalid option: $1" >&2
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usage
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;;
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esac
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done
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function run_sql_script {
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local SCRIPT=$1
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psql -e -U "$DB_USER" $DB_HOST_OPT -d "$DB_NAME" --set ON_ERROR_STOP=1 < "$SCRIPT"
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if [[ $? != 0 ]]; then
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echo "Error while executing SQL script ${SCRIPT}"
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exit 1
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fi
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}
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"${SCRIPT_DIR}"/load-geoscrub-input.sh -U "$DB_USER" $DB_HOST_OPT -d "$DB_NAME" $GEOSCRUB_INPUT_OPT
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if [[ $? != 0 ]]; then
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echo "Could not load ${DB_NAME} database with geonames.org data."
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exit 1
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fi
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echo "Scrubbing input with geonames data..."
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run_sql_script "${SCRIPT_DIR}/geonames.sql"
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echo "Scrubbing input with geovalidate data..."
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run_sql_script "${SCRIPT_DIR}/geovalidate.sql"
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echo "Input successfully scrubbed."
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if [[ -n $OUTPUT_FILE ]]; then
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echo "Saving geoscrubbed data as a CSV file to ${OUTPUT_FILE}..."
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run_sql_script "${SCRIPT_DIR}/output.geoscrub.sql" > "$OUTPUT_FILE"
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if [[ ! -w $OUTPUT_FILE ]]; then
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echo "Could not save geoscrub table contents to ${OUTPUT_FILE}"
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exit 1
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fi
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else
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echo "Scrubbed input available in the geoscrub table of the ${DB_NAME} database."
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fi
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