labkeyDocker/bin/installLabkey.sh

#!/bin/bash

. $(dirname $0)/env.sh

LABKEY=LabKey22.3.2-3-community

if [ $# -gt 0 ] ; 
then
	case $1 in
	18.1)
		LABKEY=LabKey18.1-57017.17-professional-bin;;
	18.3)
		LABKEY=LabKey18.3.3-62784.7-community-bin;;
	20.7)
		LABKEY=LabKey20.7.8-66016.22-community-bin;;
	21.1)
		LABKEY=LabKey21.11.10-11-community;;
	22.3)        
        	LABKEY=LabKey22.3.2-3-community;;
	esac;

fi;

echo "Using $LABKEY";

#full path to source
SFW_SRC=$LBDOCKER/packages/$LABKEY.tar.gz

#this is temp only
TMP_DIR=$HOME/tmp

if [ ! -d ${TMP_DIR} ] ; 
then
	mkdir ${TMP_DIR};
fi;

#is there anything relevant in $LABKEY_DIR?
if [ ! -d $LABKEY_DIR ] ; 
then
	mkdir $LABKEY_DIR;
fi;

#unpack to ${TMP_DIR}/$LABKEY
TMP_LABKEY=${TMP_DIR}/$LABKEY;

#make sure we are starting from a clean slate
if [ -d ${TMP_LABKEY} ] ; then
   rm -rf ${TMP_LABKEY};
fi;

#untar in ${TMP_DIR}
cd ${TMP_DIR} && tar xvzf ${SFW_SRC};
echo "Using distribution in ${TMP_LABKEY}";

#copy from $TMP_LABKEY to labkey space in docker
LABKEY_SRC_DIRS=("labkeywebapp" "modules" "pipeline-lib")

for d in ${LABKEY_SRC_DIRS[@]} ; 
do
   mv ${TMP_LABKEY}/$d ${LABKEY_DIR}/$d;
done;

#check if required dirs are missing and create them
LABKEY_DIRS=("files" "externalModules")

for d in ${LABKEY_DIRS[@]} ; 
do
   if [ ! -d ${LABKEY_DIR}/$d ] ; then
      mkdir ${LABKEY_DIR}/$d;
   fi;
done;

#tomcat-lib goes to tomcat8 user space in docker
mv ${TMP_LABKEY}/tomcat-lib ${TOMCAT_DIR}/lib

echo "Cleanup";
rm -rf ${TMP_LABKEY}

echo "Done"