UploadToDatabase2

#!/bin/bash
#**************************************************************
#  EPPIC Pre-Computation Script
#  Author : Kumaran Baskaran
#  Date   : 05/07/2013
#***************************************************************
set -e
help="\t\tUsage : $0 \n
	\t\t [-d <dir-path> : Directory contains downloaded files\n
	\t\t -j <file-path> : eppic jar file path\n
	\t\t -n <name> : database name (usually uniprot relese name)]\n
\t\tExample : ./Download files -o ~/Downloads "

if (($# == 0)); then
	echo "`date +%d/%m/%y-%H:%M:%S` ERROR: Script requires arguments" >&2
	echo -e $help
	exit 1;
fi

while getopts :d:j:n:h opt
do
	case $opt in 
	d) DOWNLOAD=$OPTARG;;
	j) EPPIC_JAR=$OPTARG;;
	n) DATABASE_NAME=$OPTARG;;
	h) echo -e $help;;
	\?) echo "`date +%d/%m/%y-%H:%M:%S` ERROR: Invalid option: -$OPTARG" >&2
		exit 1;;
	:) echo "`date +%d/%m/%y-%H:%M:%S` ERROR: Option -$OPTARG requires an argument." >&2
		exit 1;;
	esac
done

if [ -z $DOWNLOAD ] || [ -z $EPPIC_JAR ] || [ -z $DATABASE_NAME ]
then
	echo -e "\n`date +%d/%m/%y-%H:%M:%S` ERROR: ---------Some Options not specified correctly -------" >&2
	echo -e $help
	exit 1
fi

if [ ! -e $EPPIC_JAR ]
then
	echo -e "\t `date +%d/%m/%y-%H:%M:%S` ERROR: Couldn't find $EPPIC_JAR ..........." >&2
	exit 1
fi


if [ ! -e $DOWNLOAD/uniref100.xml.gz ]
then 
	echo "`date +%d/%m/%y-%H:%M:%S` ERROR: Couldn't find $DOWNLOAD/uniref100.xml.gz" >&2
	exit 1
fi

if [ ! -e $DOWNLOAD/taxonomy-all.tab ]
then 
	echo "`date +%d/%m/%y-%H:%M:%S` ERROR: Couldn't find $DOWNLOAD/taxonomy-all.tab" >&2
	exit 1
fi



#------------Create taxonomy table-----------------------------
table=taxonomy
# creating tables
echo "`date +%d/%m/%y-%H:%M:%S` INFO: Creating $table table..."
mysql $DATABASE_NAME <<EOF
DROP TABLE IF EXISTS $table;

CREATE TABLE $table (
 tax_id int PRIMARY KEY,
 mnemonic varchar(20),
 scientific varchar(255),
 common varchar(255),
 synonym varchar(255),
 other text,
 reviewed varchar(20),
 rank varchar(20),
 lineage text,
 parent int
 
);
EOF
#-------------------------------------------------------------
# loading data
echo "`date +%d/%m/%y-%H:%M:%S` INFO: Loading data into $table table"
mysql --enable-local $DATABASE_NAME <<EOF
LOAD DATA LOCAL INFILE '$DOWNLOAD/taxonomy-all.tab' INTO TABLE $table IGNORE 1 LINES;
SHOW WARNINGS;
EOF
echo "`date +%d/%m/%y-%H:%M:%S` INFO: Finished loading data into taxonomy."