Initialize DB during image build

.github/workflows/build.yml

@@ -74,6 +74,6 @@ jobs:
             - name: Set output variables
               id: bake_metadata
               run: |
-                  .github/workflows/extract-image-names.sh | tee -a "${GITHUB_OUTPUT}"
+                  .github/workflows/extract-image-names.sh | tee -a "${GITHUB_OUTPUT}" | awk -F'=' '{print $2}' | jq
               env:
                   BAKE_METADATA: ${{ steps.build-upload.outputs.metadata }}

docker-bake.hcl

@@ -54,22 +54,8 @@ group "default" {
   targets = "${TARGETS}"
 }
 
-target "base-meta" {
-  tags = tags("base")
-}
-target "base-with-services-meta" {
-  tags = tags("base-with-services")
-}
-target "lab-meta" {
-  tags = tags("lab")
-}
-
-target "full-stack-meta" {
-  tags = tags("full-stack")
-}
-
 target "base" {
-  inherits = ["base-meta"]
+  tags = tags("base")
   context = "stack/base"
   platforms = "${PLATFORMS}"
   args = {
@@ -78,7 +64,7 @@ target "base" {
   }
 }
 target "base-with-services" {
-  inherits = ["base-with-services-meta"]
+  tags = tags("base-with-services")
   context = "stack/base-with-services"
   contexts = {
     base = "target:base"
@@ -90,7 +76,7 @@ target "base-with-services" {
   }
 }
 target "lab" {
-  inherits = ["lab-meta"]
+  tags = tags("lab")
   context = "stack/lab"
   contexts = {
     base = "target:base"
@@ -103,7 +89,7 @@ target "lab" {
   }
 }
 target "full-stack" {
-  inherits = ["full-stack-meta"]
+  tags = tags("full-stack")
   context = "stack/full-stack"
   contexts = {
     base-with-services = "target:base-with-services"

stack/base-with-services/Dockerfile

@@ -10,13 +10,20 @@ ARG AIIDA_VERSION
 ARG PGSQL_VERSION
 ARG TARGETARCH
 
+# Location of the Postgresql DB
+# This variable is automatically picked up by initdb and pg_ctl
+# WARNING: If you change this, you have to change it in full-stack as well!
+ENV PGDATA=/home/${NB_USER}/.postgresql
+
 # Install RabbitMQ and PostgreSQL in a dedicated conda environment.
 #
 # RabbitMQ is not available on conda-forge at the time being, see:
 # https://github.com/conda-forge/rabbitmq-server-feedstock/issues/67If
 # Instead we need install erlang via apt and RabbitMQ as a "Generic Unix Build", see:
 # https://www.rabbitmq.com/install-generic-unix.html
 # Note that this version must be compatible with system's erlang version.
+# Currently installed Erlang version is 23.3, so the latest supported RMQ version is 3.9.21
+# https://www.rabbitmq.com/docs/which-erlang#old-timers
 # Note that system erlang from arm64 is already installed in the base image,
 # together with other APT dependencies to save build time.
 RUN if [ "$TARGETARCH" = "amd64" ]; then \
@@ -58,4 +65,4 @@ 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

@@ -1,30 +1,32 @@
 #!/bin/bash
 set -x
 
+if [[ -z $PGDATA ]]; then
+   echo "ERROR: PGDATA variable not set, cannot start PostgreSQL!"
+   exit 1
+fi
+
+PSQL_LOGFILE="${PGDATA}/logfile"
 # -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 ${PSQL_LOGFILE} start"
 
 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
-   ${MAMBA_RUN} ${PSQL_START_CMD}
-
+# Initialize DB directory if it does not exist
+if [[ ! -d ${PGDATA} ]]; then
+    mkdir "${PGDATA}"
+    ${MAMBA_RUN} initdb
+    echo "unix_socket_directories = '/tmp'" >> "${PGDATA}/postgresql.conf"
 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/${NB_USER}/.postgresql -R
+    chmod -R g-rwxs "${PGDATA}"
 
-    if ! ${MAMBA_RUN} ${PSQL_STATUS_CMD}; then
-       # Cleaning up the mess if Postgresql was not shutdown properly.
-       # TODO: Rotate logfile
-       echo "" > /home/${NB_USER}/.postgresql/logfile
-       rm -vf /home/${NB_USER}/.postgresql/postmaster.pid
-       ${MAMBA_RUN} ${PSQL_START_CMD}
-   fi
+    if [[ -f ${PGDATA}/logfile ]]; then
+         mv "${PSQL_LOGFILE}" "${PSQL_LOGFILE}.1" && gzip "${PSQL_LOGFILE}.1"
+    fi
+    # Cleaning up the mess if PostgreSQL was not shutdown properly.
+    rm -vf "${PGDATA}/postmaster.pid"
 fi
+
+# Start the server
+${MAMBA_RUN} ${PSQL_START_CMD}

stack/full-stack/Dockerfile

@@ -14,4 +14,10 @@ RUN fix-permissions "/home/${NB_USER}/.aiida"
 
 USER ${NB_USER}
 
+# WARNING: If you change this, you have to change it in base-with-services as well
+ENV PGDATA="/home/${NB_USER}/.postgresql"
+
+# Initialize the database
+RUN mamba run -n aiida-core-services initdb
+
 WORKDIR "/home/${NB_USER}"