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Merge pull request #58 from FDA-MyStudies/fb_ubu_psql_15-16
New Features - LabKey start/stop script and on Ubuntu - provide method to install latest Postgresql versions
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‎install-labkey.bash‎

Lines changed: 64 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -237,6 +237,8 @@ function step_default_envs() {
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POSTGRES_PROVISION_REMOTE_DB="${POSTGRES_PROVISION_REMOTE_DB:-FALSE}"
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POSTGRES_REMOTE_ADMIN_USER="${POSTGRES_REMOTE_ADMIN_USER:-postgres_admin}"
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POSTGRES_REMOTE_ADMIN_PASSWORD="${POSTGRES_REMOTE_ADMIN_PASSWORD:-}"
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# two digit Postgresql version other than distro-repo default - this is supported for Ubuntu only - example values "15" or "16"
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POSTGRES_VERSION="${POSTGRES_VERSION:-}"
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241243
# smtp env vars
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SMTP_HOST="${SMTP_HOST:-localhost}"
@@ -654,8 +656,7 @@ function step_postgres_configure() {
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fi
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;;
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657-
\
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_rhel)
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_rhel)
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if [ ! -e "/etc/yum.repos.d/pgdg-redhat-all.repo" ]; then
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sudo yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
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# Disable the built-in PostgreSQL module:
@@ -685,43 +686,58 @@ function step_postgres_configure() {
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;;
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_ubuntu)
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# TODO add platform version for 20.04 only
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# for version 11
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# Create the file repository configuration:
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# sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
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# Import the repository signing key:
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# wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get update
696-
# Postgresql 12 included in Ubuntu 20.04
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# Postgresql 12 included in Ubuntu 20.04 APT repo - otherwise install from Postgresql repos
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if [ "$POSTGRES_SVR_LOCAL" == "TRUE" ]; then
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if [ "$(platform_version)" == "20.04" ]; then
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-12
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if [[ -n $POSTGRES_VERSION && $POSTGRES_VERSION != "12" ]]; then
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sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
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wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get update
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install "postgresql-$POSTGRES_VERSION"
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else
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-12
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fi
700701
fi
701-
# Postgresql 14 included in Ubuntu 22.04
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# Postgresql 14 included in Ubuntu 22.04 APT repo - otherwise install from Postgresql repos
702703
if [ "$(platform_version)" == "22.04" ]; then
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-14
704+
if [[ -n $POSTGRES_VERSION && $POSTGRES_VERSION != "14" ]]; then
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sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
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wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get update
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install "postgresql-$POSTGRES_VERSION"
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else
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sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-14
711+
fi
704712
fi
705-
# Not needed for conical postgresql package
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#if [ ! -f /var/lib/postgresql/12/main/PG_VERSION ]; then
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# /usr/pgsql-11/bin/postgresql-11-setup initdb
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#fi
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sudo systemctl enable postgresql
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sudo systemctl start postgresql
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sudo -u postgres psql -c "create user $POSTGRES_USER password '$POSTGRES_PASSWORD';"
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sudo -u postgres psql -c "create database $POSTGRES_DB with owner $POSTGRES_USER;"
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sudo -u postgres psql -c "revoke all on database $POSTGRES_DB from public;"
715-
# This may not be needed on ubuntu
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#sed -i 's/host all all 127.0.0.1\/32 ident/host all all 127.0.0.1\/32 md5/' /etc/postgresql/12/main/pg_hba.conf
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sudo systemctl restart postgresql
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console_msg "Postgres Server and Client Installed ..."
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else
720722
if [ "$(platform_version)" == "20.04" ]; then
721-
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-client-12
723+
if [[ -n $POSTGRES_VERSION && $POSTGRES_VERSION != "12" ]]; then
724+
sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
725+
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
726+
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get update
727+
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install "postgresql-client-$POSTGRES_VERSION"
728+
else
729+
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-client-12
730+
fi
722731
fi
723732
if [ "$(platform_version)" == "22.04" ]; then
724-
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-client-14
733+
if [[ -n $POSTGRES_VERSION && $POSTGRES_VERSION != "14" ]]; then
734+
sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
735+
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
736+
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get update
737+
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install "postgresql-client-$POSTGRES_VERSION"
738+
else
739+
sudo DEBIAN_PRIORITY=critical DEBIAN_FRONTEND=noninteractive apt-get -y install postgresql-client-14
740+
fi
725741
fi
726742
console_msg "Postgres Client Installed ..."
727743
fi
@@ -906,7 +922,7 @@ function step_tomcat_service_embedded() {
906922
fi
907923

908924
}
909-
925+
# shellcheck disable=SC2120
910926
function step_tomcat_service_standard() {
911927
if _skip_step "${FUNCNAME[0]/step_/}"; then return 0; fi
912928

@@ -960,6 +976,30 @@ function step_tomcat_service_standard() {
960976
fi
961977
fi
962978

979+
# Create Labkey Service script - prevents unexpected shutdown of LabKey service during upgrades etc.
980+
NewScript="$TOMCAT_INSTALL_HOME/bin/labkey_service.sh"
981+
(
982+
/bin/cat <<-HERE_LABKEY_SERVICE_SCRIPT
983+
#!/usr/bin/env bash
984+
985+
OPERATION="\$1"
986+
987+
if [[ "\$OPERATION" == 'stop' ]]; then
988+
# wait for labkey upgrade to complete before stopping tomcat
989+
LOCKFILE="$LABKEY_INSTALL_HOME/labkeyUpgradeLockFile"
990+
991+
while [ -f "\$LOCKFILE" ]; do
992+
sleep 3
993+
done
994+
995+
fi
996+
997+
"$TOMCAT_INSTALL_HOME/bin/catalina.sh" \$@
998+
999+
HERE_LABKEY_SERVICE_SCRIPT
1000+
) >"$NewScript"
1001+
chmod 755 "$NewScript"
1002+
9631003
# Create Standard Tomcat Systemd service file -
9641004

9651005
#create tomcat_lk systemd service file
@@ -982,8 +1022,8 @@ function step_tomcat_service_standard() {
9821022
OOMScoreAdjust=-500
9831023
9841024
985-
ExecStart=$TOMCAT_INSTALL_HOME/bin/catalina.sh start
986-
ExecStop=$TOMCAT_INSTALL_HOME/bin/catalina.sh stop
1025+
ExecStart=$TOMCAT_INSTALL_HOME/bin/labkey_service.sh start
1026+
ExecStop=$TOMCAT_INSTALL_HOME/bin/labkey_service.sh stop
9871027
SuccessExitStatus=0 143
9881028
Restart=on-failure
9891029
RestartSec=2

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