70 lines
1.6 KiB
Bash
70 lines
1.6 KiB
Bash
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#! /usr/bin/env bash
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set -e
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# Load config file
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config_filepath="./config/analyzer.conf"
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if [ -f "$config_filepath" ]; then
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source "$config_filepath"
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else
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echo "Config file not found: $config_filepath"
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exit 1
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fi
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# Check if database location is specified
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if [ -z "$DATABASE" ]; then
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echo "DATABASE location not specified"
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echo "Defaults to ./var/db.sqlite"
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DATABASE="./var/db.sqlite"
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fi
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# Check if species list is specified
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if [ -z "$SPECIES_LIST" ]; then
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echo "SPECIES_LIST location not specified"
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exit 1
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fi
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function insert_taxa()
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{
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for taxon in "$(cat $SPECIES_LIST)"; do
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taxon_scientific_name=$(echo $taxon | cut -d'_' -f1)
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taxon_common_name=$(echo $taxon | cut -d'_' -f2)
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if $(taxon_exists $taxon_scientific_name); then
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echo "Taxon already exists: $taxon_scientific_name"
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else
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echo "Inserting taxon: $taxon_scientific_name"
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statement="INSERT INTO taxon (scientific_name, common_name) VALUES ('$taxon_scientific_name', '$taxon_common_name')"
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echo $statement
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result=$(sqlite3 "$DATABASE" "$statement")
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echo "$result"
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fi
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done
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}
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function taxon_exists()
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{
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taxon_scientific_name="$1"
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statement="SELECT scientific_name FROM taxon WHERE scientific_name='$taxon_scientific_name'"
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result=$(sqlite3 "$DATABASE" "$statement")
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if [ -z "$result" ]; then
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return 1
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else
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return 0
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fi
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}
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function purge_taxa()
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{
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statement="DELETE FROM taxon"
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result=$(sqlite3 "$DATABASE" "$statement")
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echo "$result"
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}
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function main()
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{
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purge_taxa
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insert_taxa
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}
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main
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