gat-cli

#!/bin/bash
# shellcheck disable=SC2207,SC2155

search_dir() {
	q="$(find -name $1 -type d  2>/dev/null| wc -l)"
	if (( q > 0 )); then
		echo 1
	else
		echo 0
	fi
}

dir_exists() {
	if [[ -d "$1" ]]; then
		echo 1
	else
		echo 0
	fi
}

path_exists() {
	if [[ -f "$1" ]]; then
		echo 1
	else
		echo 0
	fi
}

# Grep through user's files in their home directory for some string.
str_exists() {
	location="${2:-*}"
	q="$(grep "$1" -Ri $location 2>/dev/null| wc -l)"
	if (( q > 0 )); then
		echo 1
	else
		echo 0
	fi
}

service_state() {
	q=$(timeout 3 systemctl status "$1" 2>/dev/null | grep Active | awk '{print $2}')
	if [[ "$q" == "" ]]; then
		echo 0
	else
		echo 1
	fi
}

db_exists() {
	q=$(timeout 3 sudo -u postgres psql -l 2>/dev/null| grep "$1" | wc -l)
	if (( q > 0 )); then
		echo 1
	else
		echo 0
	fi
}
curl_responds() {
	q=$(timeout 3 curl --silent -k "$1" 2>/dev/null| wc -c)
	if (( q > 0 )); then
		echo 1
	else
		echo 0
	fi
}

cmd_exists() {
	if ! command -v "$1" &> /dev/null; then
		echo 0
	else
		echo 1
	fi
}

prettify() {
	cat | sed 's/1/✔ /g;s/0/✘ /g;s/2/✅/g'
}

unified-progress() {
	x=$(cat)
	# Are there any zeros
	if [[ "$x" == *"0"* ]]; then
		# If there are any ones
		if [[ "$x" == *"1"* ]]; then
			# Mixed
			echo 2
		else
			# Otherwise it's only zeros
			echo 0
		fi
	else
		echo 1
	fi
}

_status-singularity() {
	local -a r=()
	r[0]=$(cmd_exists singularity)
	echo "${r[@]}"
}

_status-ephemeris() {
	local -a r=()
	r[0]=$(dir_exists ~/ephemeris_venv)
	echo "${r[@]}"
}

_status-datalibs() {
	local -a r=()
	r[0]=$(dir_exists /libraries/)
	echo "${r[@]}"
}

_status-cluster() {
	local -a r=()
	r[0]=$(service_state munge)
	r[1]=$(service_state slurmd)
	r[2]=$(service_state slurmctld)
	r[3]=$(str_exists slurm-drmaa1)
	r[4]=$(str_exists DRMAA_LIBRARY_PATH)
	echo "${r[@]}"
}

_status-mapping() {
	local -a r=()
	r[0]=$(str_exists cpus-per-task=2)
	r[1]=$(str_exists dynamic_admin_only)
	r[2]=$(str_exists 'upper_bound')
	r[3]=$(str_exists '<resources>')
	echo "${r[@]}"
}

_status-metrics() {
	local -a r=()
	r[0]=$(str_exists job_metrics_conf.xml.j2)
	echo "${r[@]}"
}

_status-storage() {
	local -a r=()
	r[0]=$(str_exists object_store_config_file)
	r[1]=$(str_exists atosatto.minio)
	r[2]=$(str_exists dropbox)
	echo "${r[@]}"
}

_status-gxadmin() {
	local -a r=()
	r[0]=$(str_exists usegalaxy_eu.gxadmin)
	r[1]=$(cmd_exists gxadmin)
	echo "${r[@]}"
}

_status-monitoring() {
	local -a r=()
	r[0]=$(service_state influxdb)
	r[1]=$(service_state grafana-server)
	r[2]=$(service_state telegraf)
	echo "${r[@]}"
}

_status-gxit() {
	local -a r=()
	r[0]=$(service_state galaxy-gie-proxy)
	echo "${r[@]}"
}

_status-tiaas() {
	local -a r=()
	r[0]=$(service_state tiaas)
	echo "${r[@]}"
}

gat_status() { # [Admin] Get an overview of ALL tutorials not just one.
	# day 1
	local ansible=$(_status-ansible | unified-progress)
	local galaxy=$(_status-galaxy | unified-progress)
	# day 2
	local singularity=$(_status-singularity | unified-progress)
	local ephemeris=$(_status-ephemeris | unified-progress)
	local cvmfs=$(_status-cvmfs | unified-progress)
	local datalibs=$(_status-datalibs | unified-progress)
	# day 3
	local cluster=$(_status-cluster | unified-progress)
	local mapping=$(_status-mapping | unified-progress)
	local metrics=$(_status-metrics | unified-progress)
	# day 4
	local pulsar=$(_status-pulsar | unified-progress)
	local storage=$(_status-storage | unified-progress)
	local gxadmin=$(_status-gxadmin | unified-progress)
	local monitoring=$(_status-monitoring | unified-progress)
	# day 5
	local gxit=$(_status-gxit)
	local tiaas=$(_status-tiaas)

	echo -n "$(hostname -f | cut -d. -f1-2)	"
	echo "M $ansible$galaxy	T $singularity$ephemeris$cvmfs$datalibs	W $cluster$mapping$metrics	R $pulsar$storage$gxadmin$monitoring	F $gxit$tiaas" | prettify
}

gat_status-raw() {
	# day 1
	local ansible=$(_status-ansible)
	local galaxy=$(_status-galaxy)
	# day 2
	local singularity=$(_status-singularity)
	local ephemeris=$(_status-ephemeris)
	local cvmfs=$(_status-cvmfs)
	local datalibs=$(_status-datalibs)
	# day 3
	local cluster=$(_status-cluster)
	local mapping=$(_status-mapping)
	local metrics=$(_status-metrics)
	# day 4
	local pulsar=$(_status-pulsar)
	local storage=$(_status-storage)
	local gxadmin=$(_status-gxadmin)
	local monitoring=$(_status-monitoring)
	# day 5
	local gxit=$(_status-gxit)
	local tiaas=$(_status-tiaas)

	echo -n "$(hostname -f | cut -d. -f1-2)	"
	echo "M|$ansible|$galaxy	T|$singularity|$ephemeris|$cvmfs|$datalibs	W|$cluster|$mapping|$metrics	R|$pulsar|$storage|$gxadmin|$monitoring	F|$gxit|$tiaas"
}

gat_status-sum() {
	# day 1
	local ansible=$(_status-ansible)
	local galaxy=$(_status-galaxy)
	# day 2
	local singularity=$(_status-singularity)
	local ephemeris=$(_status-ephemeris)
	local cvmfs=$(_status-cvmfs)
	local datalibs=$(_status-datalibs)
	# day 3
	local cluster=$(_status-cluster)
	local mapping=$(_status-mapping)
	local metrics=$(_status-metrics)
	# day 4
	local pulsar=$(_status-pulsar)
	local storage=$(_status-storage)
	local gxadmin=$(_status-gxadmin)
	local monitoring=$(_status-monitoring)
	# day 5
	local gxit=$(_status-gxit)
	local tiaas=$(_status-tiaas)

	echo -n "$(hostname -f | cut -d. -f1-2)	"
	echo "$ansible $galaxy $singularity $ephemeris $cvmfs $datalibs $cluster $mapping $metrics $pulsar $storage $gxadmin $monitoring $gxit $tiaas" | sed 's/ / + /g' | bc
}

_status-ansible() {
	local -a r=()
	r[0]=$(str_exists 'Copy a file to the' .)
	if [[ "${r[0]}" == "0" ]]; then
		# Maybe they typo'd it? Test the output file.
		r[0]=$(path_exists /tmp/test.txt)
	fi

	r[1]=$(str_exists '^server_name:')
	r[2]=$(search_dir geerlingguy.memcached)
	r[3]=$(search_dir secret_group_vars)
	echo "${r[@]}"
}

gat_status-ansible() { # [Admin] Check status of ansible training
	local -a r=($(_status-ansible | prettify))
	echo "$(hostname)	basic ${r[0]} template ${r[1]} roles ${r[2]} secrets ${r[3]}"
}

_status-galaxy() {
	local -a r=()
	r[0]=$(service_state postgresql)
	r[1]=$(db_exists galaxy)
	# So this check works, then later reverts. Just disable it. It's more confusing than useful.
	#r[2]=$(curl_responds http://localhost:8080/api/version)
	r[2]=$(service_state galaxy)
	r[3]=$(service_state nginx)
	r[4]=$(curl_responds https://localhost:443/api/version)
	echo "${r[@]}"
}

gat_status-galaxy() { # [Admin] Check status of ansible-galaxy training
	local -a r=($(_status-galaxy | prettify))
	echo "$(hostname)	postgres ${r[0]} ${r[1]} SysD-gxy ${r[3]} SysD-nginx ${r[4]} galaxy(ssl) ${r[5]}"
}

_status-cvmfs() {
	local -a r=()
	r[0]=$(search_dir galaxyproject.cvmfs)
	r[1]=$(dir_exists /cvmfs/)
	r[2]=$(str_exists /cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml)
	echo "${r[@]}"
}
gat_status-cvmfs() { # [Admin] Check status of cvmfs training
	local -a r=($(_status-cvmfs | prettify))
	echo "$(hostname)	reqs ${r[0]} /cvmfs/ ${r[1]} gxconf ${r[2]}"
}

_status-pulsar() {
	local -a r=()
	r[0]=$(search_dir galaxyproject.pulsar)
	r[1]=$(str_exists private_token) # group var
	r[2]=$(str_exists libcurl4-openssl-dev)
	r[3]=$(str_exists PulsarRESTJobRunner)
	echo "${r[@]}"
}
gat_status-pulsar() { # [Admin] Check status of pulsar training
	local -a r=($(_status-pulsar | prettify))
	echo "$(hostname)	reqs ${r[0]} groupvars ${r[1]} playbook ${r[2]} jobconf ${r[3]}"
}

usage() {
	echo "Galaxy Admin Training (gat) tool:"
	echo
	grep '^gat_.*()\s*{\s*# ' $0 | sed "s/gat_/  gat /g;s/().*#/\t/;"
	echo
	exit 1;
}

cmd="$1"; shift;
if [[ "$cmd" == "" ]]; then
	usage
else
	# Check that FN exists
	LC_ALL=C type "gat_$cmd" 2> /dev/null | grep -q 'function'
	ec=$?

	# If missing, exit with help
	if (( ec != 0 )); then
		echo "Unknown command!"
		usage
	fi

	gat_$cmd $@
fi