prepare_data.sh

#! /bin/bash

# Configuration
DB_NAME=deepdive_titles
DB_USER=czhang
DB_PASSWORD="Password is set via the PGPASSWORD environment variable"

cd `dirname $0`
BASE_DIR=`pwd`

#dropdb -U $DB_USER deepdive_titles
#createdb -U $DB_USER deepdive_titles

psql -U $DB_USER -c "drop schema if exists public cascade; create schema public;" $DB_NAME

psql -U $DB_USER -c "CREATE TABLE docids(
	id bigserial primary key,
	docid text,
	folder text);" $DB_NAME

psql -U $DB_USER -c "CREATE TABLE documents(
	id bigserial primary key,
	docid text,
	document text);" $DB_NAME

psql -U $DB_USER -c "CREATE TABLE sentences(
	id bigserial primary key,
	docid text,
	sentid text,
	sentence text);" $DB_NAME

psql -U $DB_USER -c "CREATE TABLE drug_mentions(
	id bigserial primary key,
	docid text,
	sentid text,
	mid text,
	start_wid int,
	end_wid int,
	type text,
	is_correct boolean,
	repr text,
	features text[],
	object text);" $DB_NAME

psql -U $DB_USER -c "CREATE TABLE gene_mentions(
	id bigserial primary key,
	docid text,
	sentid text,
	mid text,
	start_wid int,
	end_wid int,
	type text,
	is_correct boolean,
	repr text,
	features text[],
	object text);" $DB_NAME

psql -U $DB_USER -c "CREATE TABLE relations(
	id bigserial primary key,
	type text,
	mid1 text,
	mid2 text,
	is_correct boolean,
	features text[]);" $DB_NAME