getMeta

#!/bin/bash

###################################################################################
# getMeta: Get metadata for a Cromwell workflow run                               #
# Copyright (C) 2023  Heather Ward - DNAstack                                     #
#                                                                                 #
# This program is free software; you can redistribute it and/or                   #
# modify it under the terms of the GNU General Public License                     #
# as published by the Free Software Foundation, version 2 of the                  #
# License.                                                                        #
#                                                                                 #
# This program is distributed in the hope that it will be useful,                 #
# but WITHOUT ANY WARRANTY; without even the implied warranty of                  #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                   #
# GNU General Public License for more details.                                    #
#                                                                                 #
# You should have received a copy of the GNU General Public License               #
# along with this program; if not, write to the Free Software                     #
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA. #
###################################################################################

IFS=$'\n'

set -euo pipefail

usage() {
cat << EOF

	Get metadata for a given workflow
	Defaults to using Cromwell running at localhost:8000
		Set and export CROMWELL_URL to target a different Cromwell location

	Usage: $(basename "${0}") [OPTIONS] workflow_id

	OPTIONS
		-h		Display this message and exit
		-r		Raw output
		-s		Save to a file name \${wf_id}.meta.json rather than outputting to stdout

EOF
}

while getopts "hrs" OPTION; do
	case ${OPTION} in
		h) usage; exit 1;;
		r) RAW=true;;
		s) SAVE=true;;
		\?) usage; exit 1;;
	esac
done

RAW=${RAW:-}
SAVE=${SAVE:-}
CROMWELL_URL=${CROMWELL_URL:-localhost:8000}

if [[ "${#}" -eq 0 ]]; then
	usage
	err "Must provide workflow ID"
	exit 1
else
	WORKFLOW_ID=${*: -1}
fi

if [[ "${RAW}" == "true" ]]; then
	curl \
		-s \
		-X GET \
		-H "accept: application/json" \
		"${CROMWELL_URL}/api/workflows/v1/${WORKFLOW_ID}/metadata?expandSubWorkflows=false"
elif [[ "${SAVE}" == "true" ]]; then
	curl \
		-X GET \
		-H "accept: application/json" \
		"${CROMWELL_URL}/api/workflows/v1/${WORKFLOW_ID}/metadata?expandSubWorkflows=false" \
		--output "${WORKFLOW_ID}.meta.json"
else
	curl \
		-X GET \
		-H "accept: application/json" \
		"${CROMWELL_URL}/api/workflows/v1/${WORKFLOW_ID}/metadata?expandSubWorkflows=false" \
	| jq
fi