checksum.template

#!/bin/bash

echo
echo "Begin debug messages from checksum.template"
echo

export PATH=$PATH:"$HOME/.aspera/connect/bin"

# get UUID and SRA number
UUID=${UUID}
SRA_NUM=${SRA}
AGAVE_FILE=${AGAVE_URL}
EXTERNAL_URL=${URL}
SRA_PATH="./SRA/"

FILE_PATH=""

echo "INPUT"
echo
echo "UUID: ${UUID}"
echo "SRA_NUM: ${SRA}"
echo "AGAVE_FILE: ${AGAVE_URL}"
echo "EXTERNAL_URL: ${URL}"
echo

echo "DEBUG"
echo

# internal agave file provided
if [ ${AGAVE_FILE} != "" ]; then

	echo "Internal agave file provided."
	echo "FILE_PATH: ${AGAVE_FILE}"
	echo

	FILE_PATH=${AGAVE_FILE}
else
	# SRA number provided
	if [ ${SRA_NUM} != "" ];then

		echo "SRA number provided."
		echo "SRA_NUM: ${SRA_NUM}"
		echo

		echo "Make aspera executable."
		echo "$ chmod 755 ./bin/aspera.sh"
		echo

		chmod 755 ./bin/aspera.sh

		echo "Download SRA data using aspera."
		echo "$ ./bin/aspera.sh ${SRA_NUM} ${SRA_PATH}"
		echo

		# Downloading file
		./bin/aspera.sh ${SRA_NUM} ${SRA_PATH}

		# Running checksum and update metadata
		if [ $? -eq 0 ]; then
			echo "Aspera exited successfully."
			echo

			FILE_PATH="./SRA/${SRA_NUM}.sra"
		else
			echo "Aspera did not exit successfully."
			echo "Exiting job with error code ${?}"

			echo
			echo "End debug messages from checksum.template"
			echo

			exit $?
		fi
	else
		# external file URL provided
		if [ ${EXTERNAL_URL} != "" ]; then

			echo "External URL provided."
			echo "EXTERNAL_URL: ${EXTERNAL_URL}"
			echo

			echo "Download external data."
			echo "$ wget ${EXTERNAL_URL}"
			echo

			# Download external file
			wget ${EXTERNAL_URL}

			if [ $? -eq 0 ]; then
				echo "wget exited successfully."
				echo

				FILE_PATH="${EXTERNAL_URL##*/}"
			else
				echo "wget did not exit successfully."
				echo "Exiting job with error code ${?}"

				echo
				echo "End debug messages from checksum.template"
				echo

				exit $?
			fi
		else
			echo 'No input of file match!'

			echo
			echo "End debug messages from checksum.template"
			echo

			exit 1
		fi
	fi
fi

echo "FILE_PATH: ${FILE_PATH}"
echo

if [ ! -f "${FILE_PATH}" ]; then
        echo 'File not found! Please confirm the input.'
		echo "Exiting with error code 1"

		echo
		echo "End debug messages from checksum.template"
		echo

        exit 1
fi

md5=($(md5sum ${FILE_PATH}))
lastChecksumUpdated=$(date '+%Y-%m-%d %X')

echo "checksum: ${md5}"
echo "lastChecksumUpdated: ${lastChecksumUpdated}"
echo

# echo "Post the checksum to requestbin."
# echo "$ curl -k --data \"UUID=${UUID}&checksum=${md5}&lastChecksumUpdated=${lastChecksumUpdated}\" http://requestb.in/v0cdvwv0"
# echo

# post to requestbin, used for development
# curl -k --data "UUID=${UUID}&checksum=${md5}&lastChecksumUpdated=${lastChecksumUpdated}" http://requestb.in/v0cdvwv0

echo "Post the checksum to webhook."
echo "$ curl -k --data \"UUID=${UUID}&checksum=${md5}&lastChecksumUpdated=${lastChecksumUpdated}\" https://identifierservices.org/webhook/update_checksum"
echo

# post the checksum to webhook
curl -k --data "UUID=${UUID}&checksum=${md5}&lastChecksumUpdated=${lastChecksumUpdated}" https://identifierservices.org/webhook/update_checksum

if [ $? -eq 0 ]; then
	echo "curl exited successfully."
	echo
else
	echo "curl did not exit successfully."
	echo
fi

echo "Removing file."
echo "rm ${FILE_PATH}"
echo

rm ${FILE_PATH}

echo "Removing directory."
echo "rm -rf SRA"
echo

rm -rf SRA

echo "Exiting error code 0"

echo
echo "End debug messages from checksum.template"
echo

exit 0