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caratekit.sh
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#!/usr/bin/env bash
# Debug if required
# set -xv
# The following ensures the script to stop on errors
set -e
shopt -s expand_aliases
# Rule: Two newlines before ###, none at end except for the very end
# Find out which caratekit this is, will be needed later
caratekit_install=`which caratekit.sh` || caratekit_install=""
[[ -n ${caratekit_install} ]] || unset caratekit_install
# The Carate Kid Mr. Myagi quotes, 16 fail quotes
kkfailquotes=( \
"No such thing as bad student, only bad teacher. Teacher say, student do." \
"Here are the 2 Rules of Miyagi-Ryu Carate. Rule Number 1: 'Carate for defense only.' Rule Number 2: 'First learn rule number 1.'" \
"We make sacred pact. I promise teach carate to you, you promise learn. I say, you do, no questions." \
"Never trust spiritual leader who cannot dance." \
"Lesson not just carate only. Lesson for whole life. Whole life have a balance. Everything be better." \
"Walk on road, hm? Walk left side, safe. Walk right side, safe. Walk middle, sooner or later get squish just like grape." \
"Daniel-San, lie become truth only if person wanna believe it." \
"Wax on, wax off. Wax on, wax off." \
"If carate used defend honor, defend life, carate mean something. If carate used defend plastic metal trophy, carate no mean nothing." \
"We make sacred pact. I promise teach carate to you, you promise learn. I say, you do, no questions." \
"Miyagi: Oh, Daniel-san, you too much by self, not good." \
"Better learn balance. Balance is key. Balance good, carate good. Everything good. Balance bad, better pack up, go home. Understand?" \
"Never put passion in front of principle, even if you win, you’ll lose." \
"Only root carate come from Miyagi. Just like bonsai choose own way grow because root strong you choose own way do carate same reason." \
"Either you carate do 'yes' or carate do 'no.' You carate do 'guess so,' (get squished) just like grape." \
"Just remember, license never replace eye, ear, and brain." \
)
# 2 sucess quotes
kksuccessquotes=( \
"If come from inside you, always right one." \
"Man who catch fly with chopstick, accomplish anything." \
)
success=0
# Preamble
echo ""
echo "#########################"
echo " Testing CARACal at home "
echo "#########################"
echo ""
echo "caratekit.sh $*"
echo ""
sya="############################" ; sya+=$'\n'
sya+=$'\n'
sya+="Caratekit system information" ; sya+=$'\n'
sya+=$'\n'
sya+="############################" ; sya+=$'\n'
sya+=$'\n'
sya+="Start time: "; sya+=`date -u`; sya+=$'\n'
sya+="Call executing: caratekit.sh $*"; sya+=$'\n'
sya+=$'\n'
sya+="############################" ; sya+=$'\n'
sya+=$'\n'
hostnamectl &>/dev/null && hostinfo=`hostnamectl | grep -Ev "Machine ID"'|'"Boot ID"` || hostinfo="Not accessible"
sya+="Host info: ";sya+=$'\n'
sya+=${hostinfo}
#sya+=$'\n'
# Control if help should be switched on
#(( $# > 0 )) || NOINPUT=1
# Default variables
FORCE=0
SS="/dev/null"
IA=5
endimessage=""
ALTERNATIVE_TEST_DATA_IDS=( "1524929477" "1524947605" "1532022061" )
SHORT_TEST_DATA_IDS=( "1532022061_subset" )
SPHEVERSION="1.1.0"
# current working directory
cwd=`pwd`
argcount=0
for arg in "$@"
do
(( argcount += 1 ))
if [[ "$arg" == "--help" ]] || [[ "$arg" == "-h" ]]
then
HE=1
fi
if [[ "$arg" == "--verbose-help" ]] || [[ "$arg" == "-v" ]]
then
VE=1
fi
if [[ "$arg" == "--data-reduction-info" ]] || [[ "$arg" == "-dr" ]]
then
DR=1
fi
if [[ "$arg" == "--install" ]] || [[ "$arg" == "-i" ]]
then
IN=1
fi
if [[ "$arg" == "--home-original" ]] || [[ "$arg" == "-ho" ]]
then
HO=1
# This cannot be deleted, double security
HN=1
fi
if [[ "$arg" == "--home-workspace" ]] || [[ "$arg" == "-hw" ]]
then
HW=1
fi
if [[ "$arg" == "--home-no-delete" ]] || [[ "$arg" == "-hn" ]]
then
HN=1
fi
if [[ "$arg" == "--home-folder" ]] || [[ "$arg" == "-hf" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --home-folder or -hf switch, stopping."; kill "$PPID"; exit 1; }
CARATE_HOME_FOLDER=${!nextcount}
firstletter=`echo ${CARATE_HOME_FOLDER} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_HOME_FOLDER="${cwd}/${CARATE_HOME_FOLDER}"
fi
if [[ "$arg" == "--docker-minimal" ]] || [[ "$arg" == "-dm" ]]
then
DM=1
fi
if [[ "$arg" == "--docker-alternative" ]] || [[ "$arg" == "-da" ]]
then
DA=1
fi
if [[ "$arg" == "--docker-installation" ]] || [[ "$arg" == "-di" ]]
then
DI=1
fi
if [[ "$arg" == "--singularity-minimal" ]] || [[ "$arg" == "-sm" ]]
then
SM=1
fi
if [[ "$arg" == "--singularity-alternative" ]] || [[ "$arg" == "-sa" ]]
then
SA=1
fi
if [[ "$arg" == "--singularity-installation" ]] || [[ "$arg" == "-si" ]]
then
SI=1
fi
if [[ "$arg" == "--singularity-cache-workspace" ]] || [[ "$arg" == "-scw" ]]
then
SCW=1
fi
if [[ "$arg" == "--singularity-localcache-workspace" ]] || [[ "$arg" == "-slw" ]]
then
SLW=1
fi
if [[ "$arg" == "--singularity-tmp-workspace" ]] || [[ "$arg" == "-stw" ]]
then
STW=1
fi
if [[ "$arg" == "--stimela-pull-workspace" ]] || [[ "$arg" == "-spw" ]]
then
SPW=1
fi
if [[ "$arg" == "--singularity-cache-home" ]] || [[ "$arg" == "-sch" ]]
then
SCH=1
fi
if [[ "$arg" == "--singularity-localcache-home" ]] || [[ "$arg" == "-slh" ]]
then
SLH=1
fi
if [[ "$arg" == "--singularity-tmp-home" ]] || [[ "$arg" == "-sth" ]]
then
STH=1
fi
if [[ "$arg" == "--stimela-pull-test" ]] || [[ "$arg" == "-spt" ]]
then
SPT=1
fi
if [[ "$arg" == "--singularity-cachedir" ]] || [[ "$arg" == "-scd" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --singularity-cachedir or -scd switch, stopping."; kill "$PPID"; exit 1; }
CARATE_SINGULARITY_CACHEDIR=${!nextcount}
fi
if [[ "$arg" == "--singularity-localcachedir" ]] || [[ "$arg" == "-sld" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --singularity-localcachedir or -sld switch, stopping."; kill "$PPID"; exit 1; }
CARATE_SINGULARITY_LOCALCACHEDIR=${!nextcount}
fi
if [[ "$arg" == "--singularity-tmpdir" ]] || [[ "$arg" == "-std" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --singularity-tmpdir or -std switch, stopping."; kill "$PPID"; exit 1; }
CARATE_SINGULARITY_TMPDIR=${!nextcount}
fi
if [[ "$arg" == "--singularity-nocache" ]] || [[ "$arg" == "-snc" ]]
then
SNC=1
fi
if [[ "$arg" == "--stimela-pullfolder" ]] || [[ "$arg" == "-spf" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --stimela-pullfolder or -spf switch, stopping."; kill "$PPID"; exit 1; }
CARATE_STIMELA_PULLFOLDER=${!nextcount}
fi
if [[ "$arg" == "--stimela-delete-pullfolder" ]] || [[ "$arg" == "-sdp" ]]
then
SKP=1
fi
if [[ "$arg" == "--install-attempts" ]] || [[ "$arg" == "-ia" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --install-attempt or -ia switch, stopping."; kill "$PPID"; exit 1; }
IA=${!nextcount}
fi
if [[ "$arg" == "--container-all-workspace" ]] || [[ "$arg" == "-caw" ]]
then
SCW=1
SLW=1
STW=1
SPW=1
fi
if [[ "$arg" == "--container-all-test" ]] || [[ "$arg" == "-cat" ]]
then
SCH=1
SLH=1
STH=1
SPT=1
fi
if [[ "$arg" == "--singularity-all-workspace" ]] || [[ "$arg" == "-saw" ]]
then
SCW=1
SLW=1
STW=1
fi
if [[ "$arg" == "--singularity-all-home" ]] || [[ "$arg" == "-sah" ]]
then
SCH=1
SLH=1
STH=1
fi
if [[ "$arg" == "--use-stimela-stable" ]] || [[ "$arg" == "-us" ]]
then
US=1
fi
if [[ "$arg" == "--use-stimela-master" ]] || [[ "$arg" == "-um" ]]
then
[[ -z ${US} ]] || { echo "You can use only one of -us (--use-stimela-stable) or -um (--use-stimela-master), stopping."; kill "$PPID"; exit 1; }
UM=1
fi
if [[ "$arg" == "--install-attempts" ]] || [[ "$arg" == "-ia" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --install-attempt or -ia switch, stopping."; kill "$PPID"; exit 1; }
IA=${!nextcount}
fi
if [[ "$arg" == "--omit-stimela-reinstall" ]] || [[ "$arg" == "-os" ]]
then
ORSR=1
fi
if [[ "$arg" == "--stimela-pull-force" ]] || [[ "$arg" == "-pf" ]]
then
PF=1
fi
if [[ "$arg" == "--omit-docker-prune" ]] || [[ "$arg" == "-op" ]]
then
OP=1
fi
if [[ "$arg" == "--force" ]] || [[ "$arg" == "-f" ]]
then
FORCE=1
fi
if [[ "$arg" == "--fastsim" ]] || [[ "$arg" == "-fs" ]]
then
FS=1
fi
if [[ "$arg" == "--override" ]] || [[ "$arg" == "-or" ]]
then
OR=1
fi
if [[ "$arg" == "--keep-report-dir" ]] || [[ "$arg" == "-kr" ]]
then
KR=1
fi
if [[ "$arg" == "--keep-processing-dir" ]] || [[ "$arg" == "-kp" ]]
then
KP=1
fi
if [[ "$arg" == "--no-pull" ]] || [[ "$arg" == "-np" ]]
then
NP=1
fi
if [[ "$arg" == "--workspace" ]] || [[ "$arg" == "-ws" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --workspace or -ws switch, stopping."; kill "$PPID"; exit 1; }
CARATE_WORKSPACE=${!nextcount}
firstletter=`echo ${CARATE_WORKSPACE} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_WORKSPACE="${cwd}/${CARATE_WORKSPACE}"
fi
if [[ "$arg" == "--test-data-dir" ]] || [[ "$arg" == "-td" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --test-data-dir or -td switch, stopping."; kill "$PPID"; exit 1; }
CARATE_TEST_DATA_DIR=${!nextcount}
firstletter=`echo ${CARATE_TEST_DATA_DIR} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_TEST_DATA_DIR="${cwd}/${CARATE_TEST_DATA_DIR}"
fi
if [[ "$arg" == "--omit-copy-test-data" ]] || [[ "$arg" == "-od" ]]
then
OD=1
fi
if [[ "$arg" == "--test-data-read-only" ]] || [[ "$arg" == "-ro" ]]
then
RO=1
fi
if [[ "$arg" == "--copy-config-data-id" ]] || [[ "$arg" == "-cc" ]]
then
CC=1
fi
if [[ "$arg" == "--raw-data-id" ]] || [[ "$arg" == "-ri" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --raw-data-id or -ri switch, stopping."; kill "$PPID"; exit 1; }
CARATE_RAW_DATA_ID=${!nextcount}
fi
if [[ "$arg" == "--move-test-data" ]] || [[ "$arg" == "-md" ]]
then
MD=1
fi
if [[ "$arg" == "--input-dir" ]] || [[ "$arg" == "-id" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --input-dir or -id switch, stopping."; kill "$PPID"; exit 1; }
CARATE_INPUT_DIR=${!nextcount}
firstletter=`echo ${CARATE_INPUT_DIR} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_INPUT_DIR="${cwd}/${CARATE_INPUT_DIR}"
fi
if [[ "$arg" == "--virtualenv" ]] || [[ "$arg" == "-ve" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --virtualenv or -ve switch, stopping."; kill "$PPID"; exit 1; }
CARATE_VIRTUALENV=${!nextcount}
firstletter=`echo ${CARATE_VIRTUALENV} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_VIRTUALENV="${cwd}/${CARATE_VIRTUALENV}"
fi
if [[ "$arg" == "--omit-venv-reinstall" ]] || [[ "$arg" == "-ov" ]]
then
OV=1
fi
if [[ "$arg" == "--local_stimela" ]] || [[ "$arg" == "-lst" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --local-stimela or -lst switch, stopping."; kill "$PPID"; exit 1; }
CARATE_LOCAL_STIMELA=${!nextcount}
firstletter=`echo ${CARATE_LOCAL_STIMELA} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_LOCAL_STIMELA="${cwd}/${CARATE_LOCAL_STIMELA}"
fi
if [[ "$arg" == "--caracal-build-id" ]] || [[ "$arg" == "-cb" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --caracal-build-id or -cb switch, stopping."; kill "$PPID"; exit 1; }
CARATE_CARACAL_BUILD_ID=${!nextcount}
fi
if [[ "$arg" == "--caracal-test-id" ]] || [[ "$arg" == "-ct" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --caracal-test-id or -ct switch, stopping."; kill "$PPID"; exit 1; }
CARATE_CARACAL_TEST_ID=${!nextcount}
fi
if [[ "$arg" == "--omit-caracal-reinstall" ]] || [[ "$arg" == "-oc" ]]
then
OC=1
fi
if [[ "$arg" == "--caracal-release" ]] || [[ "$arg" == "-cr" ]]
then
CR=1
fi
if [[ "$arg" == "--omit-caracal-fetch" ]] || [[ "$arg" == "-of" ]]
then
OF=1
fi
if [[ "$arg" == "--caracal-run-prefix" ]] || [[ "$arg" == "-rp" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --caracal-run-prefix or -rp switch, stopping."; kill "$PPID"; exit 1; }
CARATE_CARACAL_RUN_PREFIX=${!nextcount}
# This is a name
# firstletter=`echo ${CARATE_CARACAL_RUN_PREFIX} | head -c 1`
# [[ ${firstletter} == "/" ]] || CARATE_CARACAL_RUN_PREFIX="${cwd}/${CARATE_CARACAL_RUN_PREFIX}"
fi
if [[ "$arg" == "--caracal-former-run" ]] || [[ "$arg" == "-cf" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --caracal-former-run or -rf switch, stopping."; kill "$PPID"; exit 1; }
CARATE_CARACAL_FORMER_RUN=${!nextcount}
# Same as before, this is a name
# firstletter=`echo ${CARATE_CARACAL_FORMER_RUN} | head -c 1`
# [[ ${firstletter} == "/" ]] || CARATE_CARACAL_FORMER_RUN="${cwd}/${CARATE_CARACAL_FORMER_RUN}"
fi
if [[ "$arg" == "--caracal-run-medifix" ]] || [[ "$arg" == "-rm" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --caracal-run-medifix or -rm switch, stopping."; kill "$PPID"; exit 1; }
CARATE_CARACAL_RUN_MEDIFIX=${!nextcount}
fi
if [[ "$arg" == "--local-caracal" ]] || [[ "$arg" == "-lc" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --local-caracal or -lc switch, stopping."; kill "$PPID"; exit 1; }
CARATE_LOCAL_CARACAL=${!nextcount}
firstletter=`echo ${CARATE_LOCAL_CARACAL} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_LOCAL_CARACAL="${cwd}/${CARATE_LOCAL_CARACAL}"
fi
if [[ "$arg" == "--config-source" ]] || [[ "$arg" == "-cs" ]]
then
(( nextcount=argcount+1 ))
(( $nextcount <= $# )) || { echo "Argument expected for --config-source or -cs switch, stopping."; kill "$PPID"; exit 1; }
CARATE_CONFIG_SOURCE=${!nextcount}
firstletter=`echo ${CARATE_CONFIG_SOURCE} | head -c 1`
[[ ${firstletter} == "/" ]] || CARATE_CONFIG_SOURCE="${cwd}/${CARATE_CONFIG_SOURCE}"
fi
if [[ "$arg" == "--keep-config-dataid" ]] || [[ "$arg" == "-kd" ]]
then
KD=1
fi
if [[ "$arg" == "--docker-sample-configs" ]] || [[ "$arg" == "-dsc" ]]
then
DSC=1
fi
if [[ "$arg" == "--singularity-sample-configs" ]] || [[ "$arg" == "-ssc" ]]
then
SSC=1
fi
# Convenience switches
if [[ "$arg" == "--caracal-datared" ]] || [[ "$arg" == "-cd" ]]
then
CD=1
OC=1
OF=1
ORSR=1
KR=1
OR=1
OD=1
KP=1
FORCE=1
fi
# if [[ "$arg" == "--small-script" ]] || [[ "$arg" == "-ss" ]]
# then
# (( nextcount=argcount+1 ))
# (( $nextcount <= $# )) || { echo "Argument expected for --small-script or -ss switch, stopping."; kill "$PPID"; exit 1; }
# SS=${!nextcount}
# firstletter=`echo ${SS} | head -c 1`
# [[ ${firstletter} == "/" ]] || SS="${cwd}/${SS}"
# fi
done
if [[ -n "$HE" ]] || [[ -n "$VE" ]]
then
echo "caratekit.sh"
echo "Testing CARACal"
echo
echo "Input via setting environment variables"
echo "(Input by appropriate switches overrides environment variables)"
echo ""
echo "Environment variables:"
echo
echo " Setting an environment variable using csh or tcsh:"
echo " > setenv variable_name \"variable_value\""
echo
echo " Setting an environment variable"
echo " using bash or sh (likely your setup):"
echo " \$ export variable_name=\"variable_value\""
echo
echo "Environmental variables recognized by this script:"
echo
echo " CARATE_WORKSPACE: Directory in which all tests are made"
echo ""
echo " CARATE_VIRTUALENV: Location of the virtualenv directory"
echo " (optional)"
echo ""
echo " CARATE_LOCAL_CARACAL: Local CARACal copy to use. If not"
echo " set, CARACal will be downloaded"
echo " from https://github.com/caracal-pipeline/caracal"
echo ""
echo " CARATE_CARACAL_BUILD_ID: Build number to test. If not set, master"
echo " will be tested"
echo ""
echo " CARATE_LOCAL_STIMELA: Location of a local stimela"
echo ""
echo " CARATE_HOME_FOLDER: Location of \$HOME during test"
echo " CARATE_SINGULARITY_CACHE: Location of \$SINGULARITY_CACHEDIR"
echo " CARATE_SINGULARITY_LOCALCACHE: Location of \$SINGULARITY_LOCALCACHEDIR"
echo " CARATE_SINGULARITY_TMPDIR: Location of \$SINGULARITY_TMPDIR"
echo " CARATE_STIMELA_PULLFOLDER: Location of \$STIMELA_PULLFOLDER"
echo ""
echo " CARATE_CARACAL_TEST_ID: Only specify if CARATE_CARACAL_BUILD_ID"
echo " is undefined. All data and installations for"
echo " a specific test will be saved in the directory"
echo " \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID."
echo " CARATE_CARACAL_TEST_ID is changed to"
echo " CARATE_CARACAL_BUILD_ID"
echo " if CARATE_CARACAL_BUILD_ID is defined."
echo ""
echo " CARATE_CARACAL_RUN_PREFIX: The name prefix of an individual carate run. Will"
echo " be automatically generated if not supplied."
echo ""
echo " CARATE_CARACAL_FORMER_RUN: Name of a previous run prefix. If set, the test"
echo " directory of this run will be renamed into"
echo " \$CARATE_CARACAL_FORMER_RUN_suffix prior to running"
echo " the test and a soft link with the name of the former"
echo " directory will be created, pointing to the current"
echo " directory."
echo ""
echo " CARATE_CARACAL_RUN_MEDIFIX: The additional identifyer for logfiles of an"
echo " individual carate run. Empty if not supplied."
echo ""
echo " CARATE_RAW_DATA_ID: Names of the measurement sets to be copied"
echo " (comma-separated list without .ms extensions)"
echo ""
echo " CARATE_TEST_DATA_DIR: Directory containing test data (ms"
echo " format)"
echo ""
echo " CARATE_INPUT_DIR: Directory containing input data"
echo " (optional)"
echo ""
echo " CARATE_CONFIG_SOURCE: Local configuration file copy to use for an"
echo " additional test"
echo ""
echo "Switches:"
echo ""
echo " --help -h Show help"
echo ""
echo " --verbose-help -v Show verbose help"
echo ""
echo " --workspace ARG -ws ARG Use ARG instead of environment variable"
echo " CARATE_WORKSPACE"
echo ""
echo " --home-original -ho Do not change the HOME environment"
echo " variable during installation test"
echo ""
echo " --home-workspace -hw Use \$CARATE_WORKSPACE/home"
echo " as home folder during caratekit test"
echo ""
echo " --home-folder ARG -hf ARG Use ARG as home folder during caratekit"
echo " test"
echo ""
echo " --home-no-delete -hn Do not delete the home folder (automati-"
echo " cally applied if --home-original or"
echo " -ho are set)"
echo ""
echo " --install-attempts -ia Allowed number of attempts to pull images,"
echo " to re-invoke pip, to run stimela pull,"
echo " etc."
echo ""
echo " --virtualenv ARG -ve ARG Use ARG instead of internal virtualenv"
echo " variable CARATE_VIRTUALENV"
echo ""
echo " --omit-venv-reinstall -ov Do not re-install the virtual environment"
echo ""
echo " --caracal-release -cr Install latest CARACal release version"
echo " Default is to install current master"
echo ""
echo " --local-caracal ARG -lc ARG Use ARG instead of environment variable"
echo " CARATE_LOCAL_CARACAL"
echo ""
echo " --omit-caracal-reinstall -oc Do not pip install caracal"
echo ""
echo " --omit-caracal-fetch -of Do not fetch or copy caracal directory"
echo " if present"
echo ""
echo " --caracal-build-id ARG -cb ARG Use ARG instead of environment variable"
echo " CARATE_CARACAL_BUILD_ID"
echo ""
echo " --use-stimela-master -um Use"
echo " pip install -U --force-reinstall -r"
echo " (...)stimela-master.txt"
echo " when installing CARACal"
echo ""
echo " --use-stimela-stable -us Use"
echo " pip install -U --force-reinstall -r"
echo " (...)stimela-last_stable.txt"
echo " when installing CARACal"
echo ""
echo " --local-stimela ARG -lst ARG Use pip install -U --force-reinstall ARG"
echo " to install a local stimela (or whatever"
echo " is in ARG) when installing CARACal"
echo ""
echo " --omit-stimela-reinstall -os Do not re-install stimela"
echo ""
echo " --stimela-pull-force -pf Use -f switch when invoking stimela pull"
echo ""
echo " --docker-installation -di Test Docker installation/install Docker"
echo " Stimela (no installation if -os is set)"
echo ""
echo " --no-pull -np Do not run stimela pull prior to running"
echo " CARACal"
echo ""
echo " --omit-docker-prune -op Do not prune system during docker install"
echo ""
echo " --singularity-installation -si Test Singularity installation/install"
echo " Singularity Stimela"
echo ""
echo " --singularity-cache-workspace -scw Use \$CARATE_WORKSPACE/.singularity/cache"
echo " as \${SINGULARITY_CACHEDIR}"
echo ""
echo " --singularity-localcache-workspace -slw Use"
echo " \$CARATE_WORKSPACE/.singularity/localcache"
echo " as \${SINGULARITY_LOCALCACHEDIR}"
echo ""
echo " --singularity-tmp-workspace -stw Use \$CARATE_WORKSPACE/.singularity/tmp"
echo " as \${SINGULARITY_TMPDIR}"
echo ""
echo " --singularity-pull-workspace -spw Use \$CARATE_WORKSPACE/stimela_pullfolder"
echo " as \${STIMELA_PULLFOLDER}"
echo ""
echo " --singularity-cache-home -sch Use \${home}/.singularity/cache"
echo " as \${SINGULARITY_CACHEDIR}"
echo " \$home=your_test_directory/.home"
echo ""
echo " --singularity-localcache-home -slh Use \${home}/.singularity/localcache"
echo " as \${SINGULARITY_LOCALCACHEDIR}"
echo " \$home=your_test_directory/.home"
echo ""
echo " --singularity-tmp-home -sth Use \${home}/.singularity/tmp"
echo " as \${SINGULARITY_TMPDIR}"
echo " \$home=your_test_directory/.home"
echo ""
echo " --singularity-nocache -snc Set \${SINGULARITY_DISABLE_CACHE}"
echo " to 'True' (otherwise unset)"
echo ""
echo " --stimela-pull-test -spt Use your_test_directory/stimela_pullfolder"
echo " as \${STIMELA_PULLFOLDER}"
echo ""
echo " --singularity-cachedir ARG -scd ARG Use ARG instead of environment variable"
echo " CARATE_SINGULARITY_CACHEDIR"
echo " Location of \$SINGULARITY_CACHEDIR"
echo ""
echo " --singularity-localcachedir ARG -sld ARG Use ARG instead of environment"
echo " variable"
echo " CARATE_SINGULARITY_LOCALCACHEDIR"
echo " Location of"
echo " \$SINGULARITY_LOCALCACHEDIR"
echo ""
echo " --singularity-tmpdir ARG -std ARG Use ARG instead of environment variable"
echo " CARATE_SINGULARITY_TMPDIR"
echo " Location of \$SINGULARITY_TMPDIR"
echo ""
echo " --stimela-pullfolder ARG -spf ARG Use ARG instead of environment variable"
echo " CARATE_STIMELA_PULLFOLDER"
echo " Location of \$STIMELA_PULLFOLDER"
echo ""
echo " --stimela-delete-pullfolder -sdp Delete the content of"
echo " \$STIMELA_PULLFOLDER"
echo " (and reinstall)"
echo ""
echo " --singularity-all-home -sah Alias for -sch -slh -sth"
echo ""
echo " --singularity-all-workspace -saw Alias for -scw -slw -stw"
echo ""
echo " --container-all-test -cat Alias for -sch -slh -sth -spt"
echo ""
echo " --container-all-workspace -caw Alias for -scw -slw -stw -spw"
echo ""
echo " --caracal-test-id ARG -ct ARG Use ARG instead of environment variable"
echo " CARATE_CARACAL_TEST_ID"
echo ""
echo " --caracal-run-prefix ARG -rp ARG Use ARG instead of environment variable"
echo " CARATE_CARACAL_RUN_PREFIX"
echo ""
echo " --caracal-former-run ARG -cf ARG Use ARG instead of environment variable"
echo " CARATE_CARACAL_FORMER_RUN"
echo ""
echo " --caracal-run-medifix ARG -rp ARG Use ARG instead of environment variable"
echo " CARATE_CARACAL_RUN_MEDIFIX"
echo ""
echo " --keep-report-dir -kr Do not delete the report directory if it"
echo " exists"
echo ""
echo " --keep-report-dir -kp Do not delete any of the content of a"
echo " project directory (input, msdir, output,"
echo " stimela_parameter_files) prior to"
echo " starting a test"
echo ""
echo " --config-source ARG -cs ARG Use ARG instead of environment variable"
echo " CARATE_CONFIG_SOURCE"
echo ""
echo " --keep-config-dataid -kd Do not autodetect measurement sets but"
echo " keep the dataid in the confic source as"
echo " it is. Only if --config-source is supplied."
echo ""
echo " --test-data-dir ARG -td ARG Use ARG instead of environment variable"
echo " CARATE_TEST_DATA_DIR"
echo ""
echo " --test-data-read-only -ro Use CARATE_TEST_DATA_DIR as rawdatadir"
echo " and do not (re-)copy any test data into"
echo " msdir"
echo ""
echo " --omit-copy-test-data -od Do not re-copy test data and preserve msdir"
echo ""
echo " --move-test-data -md Move test data instead of creating a copy"
echo ""
echo " --copy-config-data -cc Copy test data as specified in the"
echo " parameter dataid from CARATE_CONFIG_SOURCE"
echo " unless CARATE_RAW_DATA_ID is defined."
echo " Ignored if CARATE_CONFIG_SOURCE is not"
echo " defined or switches --config-source -cs"
echo " are not used"
echo ""
echo " --raw-data-id ARG -ri ARG Use ARG instead of environment variable"
echo " CARATE_RAW_DATA_ID. Note that this over-"
echo " rides --copy-config-data or -cc"
echo ""
echo " --input-dir ARG -id ARG Use ARG instead of environment variable"
echo " CARATE_INPUT_DIR"
echo ""
echo " --docker-minimal -dm Test Docker installation and test run with"
echo " minimal test configuration"
echo ""
echo " --docker-alternative -da Test Docker installation and test run with"
echo " alternative configuration carateConfig.yml"
echo ""
echo " --singularity-minimal -sm Test Singularity installation and test run"
echo " with minimal test configuration"
echo ""
echo " --singularity-alternative -sa Test Singularity installation and test run"
echo " alternative configuration carateConfig.yml"
echo ""
echo " --docker-sample-configs -dsc Check all sample configurations to pass"
echo " observation config with docker."
echo ""
echo " --singularity-sample-configs -ssc Check all sample configurations to pass"
echo " observation config with singiularity."
echo ""
echo " --override -or Override security question (showing root"
echo " directory and asking whether to proceed.)"
echo ""
echo " --fastsim -fs Omit all time-consuming steps"
echo ""
echo " --force -f Force replacement and re-installation of"
echo " all components if possible (see below)"
echo ""
echo " --caracal-datared -cd Short for -oc -of -os -kr -or -kp -od -f"
echo ""
echo ""
fi
if [[ -n "$VE" ]]
then
echo ""
echo " The script creates a root directory (Notice that all environment"
echo " variables can also be supplied via the command line)"
echo " \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID, where CARATE_WORKSPACE"
echo " is an environment variable containing the path of a parent directory"
echo " to all tests done with this script. The variable"
echo " CARATE_CARACAL_TEST_ID is identical to the environment variable"
echo " CARATE_CARACAL_BUILD_ID if that is set by the user, and has to be"
echo " supplied independently (i.e. to be defined prior to the script call"
echo " or supplied using switches --caracal-test-id or -ct) as an"
echo " environment variable if CARATE_CARACAL_BUILD_ID is not defined. The"
echo " rationale behind that is that the test directory is always linked to"
echo " a git(hub) build number if that exists. Otherwise, if"
echo " CARATE_CARACAL_BUILD_ID is not defined, the user can supply an"
echo " alternative name \$CARATE_CARACAL_TEST_ID. In the test root directory"
echo " \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID, by default a home directory"
echo " called home, a virtual environment called caracal_virtualenv, a CARACal"
echo " copy caracal, and up to six test directories are created, within which"
echo " the tests are conducted. If the --force or -f switch is set, existing"
echo " directories and installations are deleted and replaced, if not, only"
echo " those directories and files are created, which do not exist"
echo " yet. Exceptions from that rule exist. If the --omit-stimela-reinstall"
echo " or -os switch is set, a re-installation of stimela is preventedeven"
echo " if -f is set. This includes the Re-installation of the virtual"
echo " environment, the home directory, and the file .stimela in the home"
echo " directory. "
echo " The location of the home directory can be changed using environment variables"
echo " and switches. The environment variable CARATE_HOME_FOLDER defines directly the"
echo " home folder. It can be overridden by the switches --home-folder ARG or -hf ARG,"
echo " where ARG is the location of the home folder. Switch -hw defines the home"
echo " folder to be the directory home in the workspace folder. Switch --home-original"
echo " or -ho leaves the home folder as it is. The default, as said above, is to"
echo " define the home folder as \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID/home"
echo " If the option --home-no-delete or -hn is set, the home folder"
echo " is preserved. -hn is automatically set if switches --home-original or -ho are set."
echo ""
echo " If"
echo " the option --keep-report or -kr is set, the directory"
echo " \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID/report is pre-"
echo " served. Switches --omit-virtualenv-reinstall and -ov prevent the"
echo " deletion of the virtualenv, --omit-caracal-reinstall will prevent the"
echo " deletion (and re- installation of CARACal. If option"
echo " --fast-simulation (-fs) is set, only the directory"
echo " \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID/report is deleted if"
echo " option -f is set. No directories or files supplied to caratekit.sh"
echo " (including their parent directories) are deleted."
echo ""
echo " In detail (all installations in the root directory"
echo " \$CARATE_WORKSPACE/\$CARATE_CARACAL_TEST_ID):"
echo ""
echo " - a directory called home is created (if not existing or if -f is"
echo " set) and the HOME environment variable set to that home directory"
echo " unless the --keep-home or -kh switches are set."
echo ""
echo " - a python 3 virtual environment name caracal_venv is created (if"
echo " not existing or if -f is set) and activated. It is not re-created"
echo " if switches --omit-stimela-reinstall (-os) or"
echo " --omit-virtualenv-reinstall (-ov) are set."
echo ""
echo " - caracal is either downloaded to the root directory (if not"
echo " existing or if -f is set) from https://github.com/caracal-pipeline/caracal"
echo " or, if the CARATE_LOCAL_CARACAL environment variable is set,"
echo " \$CARATE_LOCAL_CARACAL is copied to the root directory if not"
echo " existing or if -f is set (notice that the directory tree should be"
echo " a valid caracal tree, ready for installation). If switches"
echo " --omit-caracal-fetch or -of are set, the sources are also not"
echo " copied across."
echo ""
echo " - the caracal version CARATE_CARACAL_BUILD_ID is checked out using"
echo " git if CARATE_CARACAL_BUILD_ID is defined. If switches"
echo " --omit-caracal-reinstall or -oc are set, this is not done"
echo ""
echo " - the latest CARACal release version is checked out and installed if"
echo " switches --caracal-release or -cr are set"
echo ""
echo " - caracal is installed via pip. If switches --omit-caracal-reinstall"
echo " or -oc are set, this is not done"
echo ""
echo " - if --use-stimela-master or -um switch is set,"
echo " caracal/stimela-master.txt is installed via pip. If switches"
echo " --omit-stimela-reinstall or -os are set, this is not done"
echo ""
echo " - if --use-stimela-stable or -us switch is set,"
echo " caracal/stimela-last_stable.txt is installed via pip. If switches"
echo " --omit-stimela-reinstall or -os are set, this is not done"
echo ""
echo " - when switches --docker-minimal, -dm, --docker-alternative, -da,"
echo " --docker-installation, -di are set, home/.stimela is removed, docker"
echo " system prune is invoked, and docker stimela is installed (stimela"
echo " build). If switches --omit-stimela-reinstall or -os are set, this is"
echo " not done"
echo ""
echo " - when switches --no-pull, -np are set, stimela pull is"
echo " not invoked for a Stimela installation, otherwise a stimela pull"
echo " is executed prior to running CARACal. If switches"
echo " --omit-stimela-reinstall or -os are set, stimela pull is not"
echo " invoked either."
echo ""
echo " - There are four environment variables connected to the use of"
echo " Singularity, which can be temporarily be replaced while "
echo " using caratekit.sh. After running caratekit.sh"
echo " they will be changed back to their original values."
echo " \$SINGULARITY_CACHEDIR, \$SINGULARITY_LOCALCACHEDIR and"
echo " \$SINGULARITY_TMPDIR are environment"
echo " variables recognized by Singularity, while"
echo " \$STIMELA_PULLFOLDER is the directory used by Stimela to store"
echo " Singularity images in. By default the values of these variables are"
echo " not changed, implying that if they are unset, they are left unset."
echo " If switch --singularity-cache-workspace or -scw is set,"
echo " \$CARATE_WORKSPACE/.singularity/cache is used"
echo " as \${SINGULARITY_CACHEDIR}"
echo " If switch --singularity-localcache-workspace or -slw is set,"
echo " \$CARATE_WORKSPACE/.singularity/localcache is used"
echo " as \${SINGULARITY_LOCALCACHEDIR}"
echo " If switch --singularity-tmp-workspace or -stw is set,"
echo " \$CARATE_WORKSPACE/.singularity/tmp is used"
echo " as \${SINGULARITY_TMPDIR}"
echo " If switch --stimela-pull-workspace or -spw is set,"
echo " \$CARATE_WORKSPACE/stimela_pullfolder is used"
echo " as \${STIMELA_PULLFOLDER}."
echo " If switch --singularity-cache-home or -sch is set,"
echo " \${home}/.singularity/cache is used as \${SINGULARITY_CACHEDIR},"
echo " where \$home denotes the home folder in the test directory."
echo " If switch --singularity-localcache-home or -slh is set,"
echo " \${home}/.singularity/localcache is used as \${SINGULARITY_LOCALCACHEDIR},"
echo " where \$home denotes the home folder in the test directory."
echo " If switch --singularity-tmp-home or -sth is set,"
echo " \${home}/.singularity/tmp is used as \${SINGULARITY_TMPDIR},"
echo " where \$home denotes the home folder in the test directory."
echo " If switch --stimela-pull-test -spt is set,"
echo " your_test_directory//stimela_pullfolder is used as"
echo " \${STIMELA_PULLFOLDER},"
echo " where your_test_directory denotes the test directory."
echo " The environment variable CARATE_SINGULARITY_CACHEDIR or the"
echo " argument ARG of switches --singularity-cachedir ARG or -scd ARG"
echo " are used to directly define \$SINGULARITY_CACHEDIR."
echo " The environment variable CARATE_SINGULARITY_LOCALCACHEDIR or the"
echo " argument ARG of switches --singularity-localcachedir ARG or -sld ARG"
echo " are used to directly define \$SINGULARITY_LOCALCACHEDIR."
echo " The environment variable CARATE_SINGULARITY_TMPDIR or the"
echo " argument ARG of switches --singularity-tmpdir ARG or -std ARG"
echo " are used to directly define \$SINGULARITY_TMPDIR."
echo " The environment variable CARATE_STIMELA_PULLFOLDER or the"
echo " argument ARG of switches --stimela-pullfolder ARG or -spf ARG"
echo " are used to directly define \$STIMELA_PULLFOLDER."
echo " The definition of the environment variables using the switches"
echo " above is mutually exclusive."
echo " If \${STIMELA_PULLFOLDER} is not defined by any switch and it"
echo " is not defined prior to invoking caratekit.sh, it defaults to"
echo " STIMELA_PULLFOLDER=\$CARATE_WORKSPACE/stimela_pullfolder"
echo " If switches --singularity-nocache or -snc are set, the"
echo " environment variable \${SINGULARITY_DISABLE_CACHE} is set to"
echo " True for the time of the caratekit run (disabling caching)"
echo " and then reset to its original value (or unset). If"
echo " --singularity-nocache or -snc are not set, the environment variable"
echo " \${SINGULARITY_DISABLE_CACHE} is unset for the duration of the"
echo " caratekit run."
echo ""
echo " - when switches --singularity-minimal, -sm,"
echo " --singularity-alternative, -se, --singularity-installation, -si"
echo " are set, home/.stimela is removed. If switches"
echo " --omit-stimela-reinstall or -os are set, this is not done"
echo ""
echo " - by default, the content of \$CARATE_STIMELA_PULLFOLDER is"
echo " not deleted. This can be prevented using the switch"
echo " --stimela-delete-pullfolder or -sdp"
echo ""
echo " - when switch --singularity-minimal or -sm is set, a directory"
echo " minimal_singularity is created (if not existing or if -f is set),"
echo " the configuration file"
echo " caracal/caracal/sample_configurations/minitestConfig.yml is copied"
echo " to that directory, all .ms files from \$CARATE_TEST_DATA_DIR are"
echo " copied into the msdir directory in the minimal_singularity"
echo " directory and minitestConfig.yml is edited to point to those .ms"
echo " files in the variable dataid, then caracal is run with"
echo " minitestConfig.yml and declared successful if certain expected"
echo " files are created (see exceptions below)."
echo ""
echo " - when switch --singularity_extended or -se is set, a directory"
echo " extended_singularity is created (if not existing or if -f is"
echo " set), the configuration file"
echo " caracal/caracal/sample_configurations/extendedConfig.yml is"
echo " copied to that directory, all .ms files from \$CARATE_TEST_DATA_DIR"
echo " are copied into the msdir directory in the extended_singularity"
echo " directory and extendedConfig.yml is edited to point to those .ms"
echo " files in the variable dataid, then caracal is run with"
echo " extendedConfig.yml and declared successful if certain expected files"
echo " are created (see exceptions using variable CARATE_RAW_DATA_ID or"
echo " switches --keep-config-dataid, -kd, --copy-config-data -cc,"
echo " --copy-data-id, -ci, --test-data-read-only, -ro below)."
echo ""
echo " - when switch --docker-minimal or -dm is set, a directory \-"
echo " minimal_docker is created (if not existing or if -f is set), the"
echo " configuration file"
echo " caracal/caracal/sample_configurations/minitestConfig.yml is copied"
echo " to that directory, all .ms files from \$CARATE_TEST_DATA_DIR are"
echo " copied into the msdir directory in the minimal_docker directory"
echo " and minitestConfig.yml is edited to point to those .ms files in the"
echo " variable dataid, then caracal is run with minitestConfig.yml and"
echo " declared successful if certain expected files are created (see"
echo " exceptions using variable CARATE_RAW_DATA_ID or switches"
echo " --keep-config-dataid, -kd, --copy-config-data -cc, --copy-data-id"
echo " -ci --test-data-read-only, -ro below)."
echo ""
echo " - when switch --docker_extended or -da is set, a directory"
echo " extended_docker is created (if not existing or if -f is set), the"
echo " configuration file"