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#!/bin/bash
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# Bash script to download geoscrub_input table dump (created by AMK) from the
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aaronmk
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# vegbien database, and load it into the geoscrub database (i.e., the
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# postgis database prepped with geonames.org data, GADM2 data, and
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# associated mapping tables).
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#
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# Won't be necessary if we end up injecting all of the geoscrubbing and
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# geovalidation functionality directly into vegbien itself. And if we
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# end up implementing this stuff as a standalone service instead, we'd
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# need to rethink (and generalize) how the input data is handled. But
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# for now, this should at least serve as a placeholder that could be
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# tweaked manually to load any arbitrary geoscrub input data table.
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#
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# Jim Regetz
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# NCEAS
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# Created Nov 2012
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#
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# Paul Sarando
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# iPlant Collaborative
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# Updated Oct 2013
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aaronmk
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# Note, to force data to download from DATA_URL, ensure the DATAFILE is deleted
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# before running this script.
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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 $0)"
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DATA_URL="http://fs.vegpath.org/exports/geoscrub_input.no_header.cols=country,stateProvince,county,decimalLatitude,decimalLongitude.csv"
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DATADIR="${HOME}/geoscrub_input"
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DATAFILE="geoscrub-corpus.csv"
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aaronmk
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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 "-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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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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DATADIR="$2"
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shift 2
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;;
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--geoscrub-input=*)
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DATADIR="${1#*=}"
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shift
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;;
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*)
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echo "Invalid option: $1" >&2
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usage
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;;
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esac
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done
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if [[ ! -d "$DATADIR" ]]; then
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echo "making directory ${DATADIR}"
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mkdir -p "$DATADIR"
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if [[ $? != 0 ]]; then
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echo "Could not create directory ${DATADIR}"
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exit 1
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fi
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fi
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if [[ ! -r "${DATADIR}/${DATAFILE}" ]]; then
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# download distinct records from vegbien
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wget -O "${DATADIR}/${DATAFILE}" "$DATA_URL"
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if [[ $? != 0 ]]; then
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echo "Could not download input to ${DATADIR}/${DATAFILE}"
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exit 1
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fi
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fi
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echo "Loading vegbien data from ${DATADIR}/${DATAFILE}"
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aaronmk
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# clear previous data
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psql -e -U "$DB_USER" $DB_HOST_OPT -d "$DB_NAME" --set ON_ERROR_STOP=1 < "${SCRIPT_DIR}/truncate.vegbien_geoscrub.sql"
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if [[ $? != 0 ]]; then
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echo "Could not clear data from vegbien_geoscrub tables."
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exit 1
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fi
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# load vegbien_geoscrub table with input data
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echo "Copying vegbien_geoscrub from ${DATADIR}/${DATAFILE}"
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psql -U "$DB_USER" $DB_HOST_OPT -d "$DB_NAME" -c "\COPY vegbien_geoscrub FROM '${DATADIR}/${DATAFILE}' WITH CSV"
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