Initialize DB during image build

stack/base-with-services/Dockerfile

@@ -9,6 +9,10 @@ WORKDIR /opt/
 ARG AIIDA_VERSION
 ARG PGSQL_VERSION
 ARG TARGETARCH
+# Location of the Postgresql DB
+# This variable is automatically picked up by initdb
+ARG PGDATA_FOLDER=/home/${NB_USER}/.postgresql
+ENV PGDATA=${PGDATA_FOLDER}
 
 # Install RabbitMQ and PostgreSQL in a dedicated conda environment.
 #
@@ -58,4 +62,4 @@ USER ${NB_USER}
 WORKDIR "/home/${NB_USER}"
 
 # Initialize the database
-RUN mamba run -n aiida-core-services initdb -D aiida_db -U aiida
+RUN mamba run -n aiida-core-services initdb

stack/base-with-services/before-notebook.d/20_start-postgresql.sh

@@ -1,36 +1,30 @@
 #!/bin/bash
-
-# Activate the conda environment with PostgreSQL installed in it.
-# conda activate pgsql
+set -x
 
 # -w waits until server is up
-PSQL_START_CMD="pg_ctl --timeout=180 -w -D /home/${NB_USER}/.postgresql -l /home/${NB_USER}/.postgresql/logfile start"
-PSQL_STOP_CMD="pg_ctl -w -D /home/${NB_USER}/.postgresql stop"
-PSQL_STATUS_CMD="pg_ctl -D /home/${NB_USER}/.postgresql status"
+PSQL_START_CMD="pg_ctl --timeout=180 -w -l ${PGDATA}/logfile start"
+PSQL_STOP_CMD="pg_ctl -w stop"
+PSQL_STATUS_CMD="pg_ctl status"
 
 MAMBA_RUN="mamba run -n aiida-core-services"
 
 # make DB directory, if not existent
-if [ ! -d /home/${NB_USER}/.postgresql ]; then
-   mkdir /home/${NB_USER}/.postgresql
-   ${MAMBA_RUN} initdb -D /home/${NB_USER}/.postgresql
-   echo "unix_socket_directories = '/tmp'" >> /home/${NB_USER}/.postgresql/postgresql.conf
+if [ ! -d ${PGDATA} ]; then
+   mkdir ${PGDATA}
+   ${MAMBA_RUN} initdb
+   echo "unix_socket_directories = '/tmp'" >> ${PGDATA}/postgresql.conf
    ${MAMBA_RUN} ${PSQL_START_CMD}
 
-# else don't
 else
     # Fix problem with kubernetes cluster that adds rws permissions to the group
     # for more details see: https://github.com/materialscloud-org/aiidalab-z2jh-eosc/issues/5
-    chmod g-rwxs /home/${NB_USER}/.postgresql -R
-
-    # stores return value in $?
-    running=true
-    ${MAMBA_RUN} ${PSQL_STATUS_CMD} || running=false
+    chmod -R g-rwxs ${PGDATA}
 
-    # Postgresql was probably not shutdown properly. Cleaning up the mess...
-    if ! $running ; then
-       echo "" > /home/${NB_USER}/.postgresql/logfile # empty log files
-       rm -vf /home/${NB_USER}/.postgresql/postmaster.pid
+    if ! ${MAMBA_RUN} ${PSQL_STATUS_CMD}; then
+       # Cleaning up the mess if Postgresql was not shutdown properly.
+       # TODO: Rotate logfile
+       echo "" > ${PGDATA}/logfile
+       rm -vf ${PGDATA}/postmaster.pid
        ${MAMBA_RUN} ${PSQL_START_CMD}
    fi
 fi

stack/base-with-services/before-notebook.d/30_start-rabbitmq-amd64.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-set -em
+set -emx
 
 RABBITMQ_DATA_DIR="/home/${NB_USER}/.rabbitmq"
 

stack/base-with-services/before-notebook.d/30_start-rabbitmq-arm64.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-set -em
+set -emx
 
 RABBITMQ_DATA_DIR="/home/${NB_USER}/.rabbitmq"
 

stack/base-with-services/before-notebook.d/41_suppress-rabbitmq-version-warning.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-set -em
+set -emx
 
 # Supress rabbitmq version warning for arm64 since
 # it is built using latest version rabbitmq from apt install.

stack/base/before-notebook.d/10_prepare-home-config.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -x
 
 # If the container is start by spawner and the home is remounted.
 # The .bashrc in HOME won't be set properly.

stack/base/before-notebook.d/40_prepare-aiida.sh

@@ -1,15 +1,12 @@
 #!/bin/bash
 
 # This script is executed whenever the docker container is (re)started.
-
-# Debugging.
 set -x
 
-# Environment.
 export SHELL=/bin/bash
 
 # Check if user requested to set up AiiDA profile (and if it exists already)
-if [[ ${SETUP_DEFAULT_AIIDA_PROFILE} == true ]] && ! verdi profile show ${AIIDA_PROFILE_NAME} &> /dev/null; then
+if [[ ${SETUP_DEFAULT_AIIDA_PROFILE} == true ]] && ! verdi profile show ${AIIDA_PROFILE_NAME} 2> /dev/null; then
     NEED_SETUP_PROFILE=true;
 else
     NEED_SETUP_PROFILE=false;
@@ -48,7 +45,7 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
       exit 1
     fi
 
-    verdi computer show ${computer_name} || verdi computer setup \
+    verdi computer setup \
         --non-interactive                                               \
         --label "${computer_name}"                                      \
         --description "this computer"                                   \
@@ -61,17 +58,13 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
     verdi computer configure core.local "${computer_name}" \
         --non-interactive                                               \
         --safe-interval 0.0
-fi
-
 
-# Show the default profile
-verdi profile show || echo "The default profile is not set."
+else
 
-# Make sure that the daemon is not running, otherwise the migration will abort.
-verdi daemon stop
+  # Migration will run for the default profile.
+  verdi storage migrate --force
 
-# Migration will run for the default profile.
-verdi storage migrate --force
+fi
 
 # Daemon will start only if the database exists and is migrated to the latest version.
-verdi daemon start || echo "AiiDA daemon is not running."
+verdi daemon start || echo "ERROR: AiiDA daemon is not running!"

stack/full-stack/Dockerfile

@@ -1,13 +1,18 @@
 # syntax=docker/dockerfile:1
+ARG PGDATA_FOLDER
 FROM base-with-services as base
+ARG PGDATA_FOLDER
 
 FROM lab
 
+ENV PGDATA=${PGDATA_FOLDER}
+
 USER root
 
 COPY --from=base /opt/config-quick-setup.yaml /opt/
 COPY --from=base "${CONDA_DIR}/envs/aiida-core-services" "${CONDA_DIR}/envs/aiida-core-services"
 COPY --from=base /usr/local/bin/before-notebook.d /usr/local/bin/before-notebook.d
+COPY --from=base ${PGDATA} ${PGDATA}
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "/home/${NB_USER}/.aiida"