From f48a799ae1ef22bd240b7175b256f8199813bd2d Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Thu, 25 Apr 2024 18:48:46 +0100
Subject: [PATCH 01/33] Reduce number of verdi invocations on startup

---
 .../base/before-notebook.d/40_prepare-aiida.sh  | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/stack/base/before-notebook.d/40_prepare-aiida.sh b/stack/base/before-notebook.d/40_prepare-aiida.sh
index 869aa3d5..41053b6c 100755
--- a/stack/base/before-notebook.d/40_prepare-aiida.sh
+++ b/stack/base/before-notebook.d/40_prepare-aiida.sh
@@ -48,7 +48,8 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
       exit 1
     fi
 
-    verdi computer show ${computer_name} || verdi computer setup \
+    # TODO: Load config from YAML file
+    verdi computer setup \
         --non-interactive                                               \
         --label "${computer_name}"                                      \
         --description "this computer"                                   \
@@ -61,17 +62,15 @@ 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
+  # Show the default profile
+  verdi profile show
+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."

From bdd8ef13cdc4e8f179cf6a3bf44ee8e2983dbbcd Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Thu, 25 Apr 2024 19:06:32 +0100
Subject: [PATCH 02/33] Set debug outputs

---
 .../base-with-services/before-notebook.d/20_start-postgresql.sh | 1 +
 .../before-notebook.d/30_start-rabbitmq-amd64.sh                | 2 +-
 .../before-notebook.d/30_start-rabbitmq-arm64.sh                | 2 +-
 .../before-notebook.d/41_suppress-rabbitmq-version-warning.sh   | 2 +-
 stack/base/before-notebook.d/10_prepare-home-config.sh          | 1 +
 5 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index 0eb685e7..fd7623ae 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -x
 
 # Activate the conda environment with PostgreSQL installed in it.
 # conda activate pgsql
diff --git a/stack/base-with-services/before-notebook.d/30_start-rabbitmq-amd64.sh b/stack/base-with-services/before-notebook.d/30_start-rabbitmq-amd64.sh
index 5c55fff3..c4b40a6e 100644
--- a/stack/base-with-services/before-notebook.d/30_start-rabbitmq-amd64.sh
+++ b/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"
 
diff --git a/stack/base-with-services/before-notebook.d/30_start-rabbitmq-arm64.sh b/stack/base-with-services/before-notebook.d/30_start-rabbitmq-arm64.sh
index 95830a49..b73be1d7 100644
--- a/stack/base-with-services/before-notebook.d/30_start-rabbitmq-arm64.sh
+++ b/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"
 
diff --git a/stack/base-with-services/before-notebook.d/41_suppress-rabbitmq-version-warning.sh b/stack/base-with-services/before-notebook.d/41_suppress-rabbitmq-version-warning.sh
index f778bbb5..df77710b 100644
--- a/stack/base-with-services/before-notebook.d/41_suppress-rabbitmq-version-warning.sh
+++ b/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.
diff --git a/stack/base/before-notebook.d/10_prepare-home-config.sh b/stack/base/before-notebook.d/10_prepare-home-config.sh
index a4d0ab70..fa9ecc3b 100644
--- a/stack/base/before-notebook.d/10_prepare-home-config.sh
+++ b/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.

From f02bc2843ebd125609c16b4c39723db3c0b3b053 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Thu, 25 Apr 2024 21:42:19 +0100
Subject: [PATCH 03/33] Cleanup 20_start-postgresql.sh

---
 .../before-notebook.d/20_start-postgresql.sh      | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index fd7623ae..6d7ea108 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -1,9 +1,6 @@
 #!/bin/bash
 set -x
 
-# Activate the conda environment with PostgreSQL installed in it.
-# conda activate pgsql
-
 # -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/${NB_USER}/.postgresql stop"
@@ -18,19 +15,15 @@ if [ ! -d /home/${NB_USER}/.postgresql ]; then
    echo "unix_socket_directories = '/tmp'" >> /home/${NB_USER}/.postgresql/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
-
-    # Postgresql was probably not shutdown properly. Cleaning up the mess...
-    if ! $running ; then
-       echo "" > /home/${NB_USER}/.postgresql/logfile # empty log files
+    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

From 6f639aa2c012dc3e138d70ea00ef6fbaa742136e Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Fri, 17 May 2024 10:29:12 +0100
Subject: [PATCH 04/33] More tweaks

---
 stack/base/before-notebook.d/40_prepare-aiida.sh | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/stack/base/before-notebook.d/40_prepare-aiida.sh b/stack/base/before-notebook.d/40_prepare-aiida.sh
index 41053b6c..5242d4e0 100755
--- a/stack/base/before-notebook.d/40_prepare-aiida.sh
+++ b/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 +45,6 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
       exit 1
     fi
 
-    # TODO: Load config from YAML file
     verdi computer setup \
         --non-interactive                                               \
         --label "${computer_name}"                                      \
@@ -68,9 +64,7 @@ else
   # Migration will run for the default profile.
   verdi storage migrate --force
 
-  # Show the default profile
-  verdi profile show
 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!"

From da9cffdecf6ec54b464b1bbe8849ca77c2132392 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 00:34:27 +0100
Subject: [PATCH 05/33] Prepare DB during build

---
 stack/base-with-services/Dockerfile | 2 +-
 stack/full-stack/Dockerfile         | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 99f0331e..70aa01ba 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -58,4 +58,4 @@ 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 -D /home/${NB_USER}/.postgresql
diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index aefe2a82..cd21b413 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -8,9 +8,10 @@ USER root
 COPY --from=base /opt/config-quick-setup.yaml /opt/
 COPY --from=base "${CONDA_DIR}/envs/aiida-core-services" "${CONDA_DIR}/envs/aiida-core-services"
 COPY --from=base /usr/local/bin/before-notebook.d /usr/local/bin/before-notebook.d
+COPY --from=base /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
 
 RUN fix-permissions "${CONDA_DIR}"
-RUN fix-permissions "/home/${NB_USER}/.aiida"
+RUN fix-permissions "/home/${NB_USER}"
 
 USER ${NB_USER}
 

From 79231b6dfbb22ffafa16912ee62eec4b8d8b6c93 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 00:56:18 +0100
Subject: [PATCH 06/33] Try without root

---
 stack/full-stack/Dockerfile | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index cd21b413..99326664 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -3,15 +3,10 @@ FROM base-with-services as base
 
 FROM lab
 
-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 /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
-
-RUN fix-permissions "${CONDA_DIR}"
-RUN fix-permissions "/home/${NB_USER}"
+COPY --from=base "/home/${NB_USER}/.postgresql" "/home/${NB_USER}/.postgresql"
 
 USER ${NB_USER}
 

From a6320de878be2f2371e0cf1dcb8c957a86d8f0c4 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 01:41:13 +0100
Subject: [PATCH 07/33] Use PGDATA

---
 stack/base-with-services/Dockerfile                          | 5 ++++-
 .../before-notebook.d/20_start-postgresql.sh                 | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 70aa01ba..5954d825 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -9,6 +9,9 @@ WORKDIR /opt/
 ARG AIIDA_VERSION
 ARG PGSQL_VERSION
 ARG TARGETARCH
+# Location of the Postgresql DB
+# This variable is automatically picked up by initdb
+ARG ENV PGDATA=/home/${NB_USER}/.posgresql
 
 # Install RabbitMQ and PostgreSQL in a dedicated conda environment.
 #
@@ -58,4 +61,4 @@ USER ${NB_USER}
 WORKDIR "/home/${NB_USER}"
 
 # Initialize the database
-RUN mamba run -n aiida-core-services initdb -D /home/${NB_USER}/.postgresql
+RUN mamba run -n aiida-core-services initdb
diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index 6d7ea108..e4466cf3 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -11,7 +11,7 @@ MAMBA_RUN="mamba run -n aiida-core-services"
 # make DB directory, if not existent
 if [ ! -d /home/${NB_USER}/.postgresql ]; then
    mkdir /home/${NB_USER}/.postgresql
-   ${MAMBA_RUN} initdb -D /home/${NB_USER}/.postgresql
+   ${MAMBA_RUN} initdb
    echo "unix_socket_directories = '/tmp'" >> /home/${NB_USER}/.postgresql/postgresql.conf
    ${MAMBA_RUN} ${PSQL_START_CMD}
 

From fac06ff02f6fd85db3ddfe756ce16d02f93391f3 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 01:53:27 +0100
Subject: [PATCH 08/33] Revert "Try without root"

This reverts commit 79231b6dfbb22ffafa16912ee62eec4b8d8b6c93.
---
 stack/full-stack/Dockerfile | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 99326664..cd21b413 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -3,10 +3,15 @@ FROM base-with-services as base
 
 FROM lab
 
+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 "/home/${NB_USER}/.postgresql" "/home/${NB_USER}/.postgresql"
+COPY --from=base /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
+
+RUN fix-permissions "${CONDA_DIR}"
+RUN fix-permissions "/home/${NB_USER}"
 
 USER ${NB_USER}
 

From b4e61457bc9206e8283f7787bee7a4672baa0ffd Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 02:00:06 +0100
Subject: [PATCH 09/33] PGDATA everywhere

---
 stack/base-with-services/Dockerfile            |  2 +-
 .../before-notebook.d/20_start-postgresql.sh   | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 5954d825..88afa65c 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -11,7 +11,7 @@ ARG PGSQL_VERSION
 ARG TARGETARCH
 # Location of the Postgresql DB
 # This variable is automatically picked up by initdb
-ARG ENV PGDATA=/home/${NB_USER}/.posgresql
+ENV PGDATA=/home/${NB_USER}/.posgresql
 
 # Install RabbitMQ and PostgreSQL in a dedicated conda environment.
 #
diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index e4466cf3..0a696354 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -2,29 +2,29 @@
 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
+if [ ! -d ${PGDATA} ]; then
+   mkdir ${PGDATA}
    ${MAMBA_RUN} initdb
-   echo "unix_socket_directories = '/tmp'" >> /home/${NB_USER}/.postgresql/postgresql.conf
+   echo "unix_socket_directories = '/tmp'" >> ${PGDATA}/postgresql.conf
    ${MAMBA_RUN} ${PSQL_START_CMD}
 
 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 g-rwxs ${PGDATA} -R
 
     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
+       echo "" > ${PGDATA}/logfile
+       rm -vf ${PGDATA}/postmaster.pid
        ${MAMBA_RUN} ${PSQL_START_CMD}
    fi
 fi

From ac248db16ac3543e191bef39108b40b8754bec63 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 02:16:11 +0100
Subject: [PATCH 10/33] back

---
 stack/full-stack/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index cd21b413..86d9430a 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -8,7 +8,7 @@ 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 /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
+#COPY --from=base /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "/home/${NB_USER}"

From 2e5ba4667c9b84393e6cccf6cd4d572786af606d Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 02:47:37 +0100
Subject: [PATCH 11/33] Fix?

---
 stack/base-with-services/Dockerfile                             | 2 +-
 .../base-with-services/before-notebook.d/20_start-postgresql.sh | 2 +-
 stack/full-stack/Dockerfile                                     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 88afa65c..7cd8bf86 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -11,7 +11,7 @@ ARG PGSQL_VERSION
 ARG TARGETARCH
 # Location of the Postgresql DB
 # This variable is automatically picked up by initdb
-ENV PGDATA=/home/${NB_USER}/.posgresql
+ENV PGDATA=/home/${NB_USER}/.postgresql
 
 # Install RabbitMQ and PostgreSQL in a dedicated conda environment.
 #
diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index 0a696354..b17ca038 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -18,7 +18,7 @@ if [ ! -d ${PGDATA} ]; then
 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 ${PGDATA} -R
+    chmod -R g-rwxs ${PGDATA}
 
     if ! ${MAMBA_RUN} ${PSQL_STATUS_CMD}; then
        # Cleaning up the mess if Postgresql was not shutdown properly.
diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 86d9430a..cd21b413 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -8,7 +8,7 @@ USER root
 COPY --from=base /opt/config-quick-setup.yaml /opt/
 COPY --from=base "${CONDA_DIR}/envs/aiida-core-services" "${CONDA_DIR}/envs/aiida-core-services"
 COPY --from=base /usr/local/bin/before-notebook.d /usr/local/bin/before-notebook.d
-#COPY --from=base /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
+COPY --from=base /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "/home/${NB_USER}"

From 50e2611456fc2338f2b64115b91ca765feeb9868 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 03:01:17 +0100
Subject: [PATCH 12/33] Pass PGDATA for full-stack

---
 stack/base-with-services/Dockerfile | 3 ++-
 stack/full-stack/Dockerfile         | 5 ++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 7cd8bf86..7d13ef78 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -11,7 +11,8 @@ ARG PGSQL_VERSION
 ARG TARGETARCH
 # Location of the Postgresql DB
 # This variable is automatically picked up by initdb
-ENV PGDATA=/home/${NB_USER}/.postgresql
+ARG PGDATA_FOLDER=/home/${NB_USER}/.postgresql
+ENV PGDATA=${PGDATA_FOLDER}
 
 # Install RabbitMQ and PostgreSQL in a dedicated conda environment.
 #
diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index cd21b413..4f64907f 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -1,14 +1,17 @@
 # syntax=docker/dockerfile:1
 FROM base-with-services as base
+ARG PGDATA_FOLDER
 
 FROM lab
+ARG PGDATA_FOLDER
+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 /home/${NB_USER}/.postgresql /home/${NB_USER}/.postgresql
+COPY --from=base ${PGDATA} ${PGDATA}
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "/home/${NB_USER}"

From be5846d926a57f41c4a456515f78cb16e64e4e28 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Tue, 21 May 2024 16:27:45 +0100
Subject: [PATCH 13/33] This?

---
 stack/full-stack/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 4f64907f..6219aeb3 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -3,7 +3,7 @@ FROM base-with-services as base
 ARG PGDATA_FOLDER
 
 FROM lab
-ARG PGDATA_FOLDER
+
 ENV PGDATA=${PGDATA_FOLDER}
 
 USER root

From e89f505f21aae5544973fb92faf886a0c450e37f Mon Sep 17 00:00:00 2001
From: Daniel Hollas <danekhollas@gmail.com>
Date: Fri, 24 May 2024 13:30:37 +0100
Subject: [PATCH 14/33] Update stack/full-stack/Dockerfile

---
 stack/full-stack/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 6219aeb3..e07c3a3c 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -1,4 +1,5 @@
 # syntax=docker/dockerfile:1
+ARG PGDATA_FOLDER
 FROM base-with-services as base
 ARG PGDATA_FOLDER
 

From 9aaa20dfb8edd398f0659ff407644d3a59d3a290 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <danekhollas@gmail.com>
Date: Fri, 24 May 2024 13:40:26 +0100
Subject: [PATCH 15/33] Update stack/full-stack/Dockerfile

---
 stack/full-stack/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index e07c3a3c..be605241 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -15,7 +15,7 @@ COPY --from=base /usr/local/bin/before-notebook.d /usr/local/bin/before-notebook
 COPY --from=base ${PGDATA} ${PGDATA}
 
 RUN fix-permissions "${CONDA_DIR}"
-RUN fix-permissions "/home/${NB_USER}"
+RUN fix-permissions "/home/${NB_USER}/.aiida"
 
 USER ${NB_USER}
 

From 163e4f29f79cac914be061401fbdd72c539c5574 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <danekhollas@gmail.com>
Date: Fri, 24 May 2024 13:55:25 +0100
Subject: [PATCH 16/33] Update stack/full-stack/Dockerfile

---
 stack/full-stack/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index be605241..4ec9b19b 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -5,6 +5,7 @@ ARG PGDATA_FOLDER
 
 FROM lab
 
+ARG PGDATA_FOLDER
 ENV PGDATA=${PGDATA_FOLDER}
 
 USER root

From e4c45e120150762295adc9840883d00ccd67391e Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Thu, 23 May 2024 12:45:18 +0100
Subject: [PATCH 17/33] Add comment about Erlang

---
 stack/base-with-services/Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 7d13ef78..0e5eab0c 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -21,6 +21,8 @@ ENV PGDATA=${PGDATA_FOLDER}
 # Instead we need install erlang via apt and RabbitMQ as a "Generic Unix Build", see:
 # https://www.rabbitmq.com/install-generic-unix.html
 # Note that this version must be compatible with system's erlang version.
+# Currently installed Erlang version is 23.3, so the latest supported RMQ version is 3.9.21
+# https://www.rabbitmq.com/docs/which-erlang#old-timers
 # Note that system erlang from arm64 is already installed in the base image,
 # together with other APT dependencies to save build time.
 RUN if [ "$TARGETARCH" = "amd64" ]; then \

From 1ac56fbc50f422b30bb60c779861bdf0e7d315a5 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Fri, 24 May 2024 14:50:23 +0100
Subject: [PATCH 18/33] Come on!

---
 stack/full-stack/Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 4ec9b19b..be605241 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -5,7 +5,6 @@ ARG PGDATA_FOLDER
 
 FROM lab
 
-ARG PGDATA_FOLDER
 ENV PGDATA=${PGDATA_FOLDER}
 
 USER root

From bdf390755a25291b4d273d8fcbe7872f7c7cea26 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Fri, 24 May 2024 14:53:03 +0100
Subject: [PATCH 19/33] Remove meta targets

---
 docker-bake.hcl | 22 ++++------------------
 1 file changed, 4 insertions(+), 18 deletions(-)

diff --git a/docker-bake.hcl b/docker-bake.hcl
index 46d8225b..44d74a55 100644
--- a/docker-bake.hcl
+++ b/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"

From c8c1cef172ccdde65c81e08c88dd4b1ad0b04720 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Fri, 24 May 2024 17:03:14 +0100
Subject: [PATCH 20/33] Preserve logfile

---
 .../before-notebook.d/20_start-postgresql.sh                 | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index b17ca038..d6d50b50 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -3,7 +3,6 @@ set -x
 
 # -w waits until server is up
 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"
@@ -17,13 +16,11 @@ if [ ! -d ${PGDATA} ]; then
 
 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 -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 "" > ${PGDATA}/logfile
+       mv ${PGDATA}/logfile ${PGDATA/logfile.1 && gzip ${PGDATA}/logfile.1
        rm -vf ${PGDATA}/postmaster.pid
        ${MAMBA_RUN} ${PSQL_START_CMD}
    fi

From 2ddeac02cee37cf0e000fc341454e5854660dfd5 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Fri, 24 May 2024 17:18:09 +0100
Subject: [PATCH 21/33] sigh

---
 stack/full-stack/Dockerfile | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index be605241..5f684a02 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -2,17 +2,16 @@
 ARG PGDATA_FOLDER
 FROM base-with-services as base
 ARG PGDATA_FOLDER
+ENV PGDATA=${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}
+COPY --from=base ${PGDATA_FOLDER} ${PGDATA_FOLDER}
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "/home/${NB_USER}/.aiida"

From 7e9c91cfed40277ab5232a51cd5484eb81df11bf Mon Sep 17 00:00:00 2001
From: Daniel Hollas <danekhollas@gmail.com>
Date: Sat, 25 May 2024 12:43:30 +0100
Subject: [PATCH 22/33] fix

---
 .../base-with-services/before-notebook.d/20_start-postgresql.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index d6d50b50..c79fba1b 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -20,7 +20,7 @@ else
 
     if ! ${MAMBA_RUN} ${PSQL_STATUS_CMD}; then
        # Cleaning up the mess if Postgresql was not shutdown properly.
-       mv ${PGDATA}/logfile ${PGDATA/logfile.1 && gzip ${PGDATA}/logfile.1
+       mv ${PGDATA}/logfile ${PGDATA}/logfile.1 && gzip ${PGDATA}/logfile.1
        rm -vf ${PGDATA}/postmaster.pid
        ${MAMBA_RUN} ${PSQL_START_CMD}
    fi

From 2d0e8f47e545e4f30f2261f4530ae5284474e639 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 17:53:36 +0100
Subject: [PATCH 23/33] remove pg_ctl status

---
 .../before-notebook.d/20_start-postgresql.sh  | 37 +++++++++++--------
 1 file changed, 21 insertions(+), 16 deletions(-)

diff --git a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
index c79fba1b..3c9a443c 100644
--- a/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
+++ b/stack/base-with-services/before-notebook.d/20_start-postgresql.sh
@@ -1,27 +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 -l ${PGDATA}/logfile start"
-PSQL_STATUS_CMD="pg_ctl 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 ${PGDATA} ]; then
-   mkdir ${PGDATA}
-   ${MAMBA_RUN} initdb
-   echo "unix_socket_directories = '/tmp'" >> ${PGDATA}/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
-    chmod -R g-rwxs ${PGDATA}
+    chmod -R g-rwxs "${PGDATA}"
 
-    if ! ${MAMBA_RUN} ${PSQL_STATUS_CMD}; then
-       # Cleaning up the mess if Postgresql was not shutdown properly.
-       mv ${PGDATA}/logfile ${PGDATA}/logfile.1 && gzip ${PGDATA}/logfile.1
-       rm -vf ${PGDATA}/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}

From d03f11b4afd806a84dcb2200421fd2ecb6027356 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 18:10:17 +0100
Subject: [PATCH 24/33] To hell with it

---
 stack/base-with-services/Dockerfile | 7 ++++---
 stack/full-stack/Dockerfile         | 8 ++++----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/stack/base-with-services/Dockerfile b/stack/base-with-services/Dockerfile
index 0e5eab0c..d941153d 100644
--- a/stack/base-with-services/Dockerfile
+++ b/stack/base-with-services/Dockerfile
@@ -9,10 +9,11 @@ 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}
+# 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.
 #
diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 5f684a02..2a10f234 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -1,17 +1,17 @@
 # syntax=docker/dockerfile:1
-ARG PGDATA_FOLDER
 FROM base-with-services as base
-ARG PGDATA_FOLDER
-ENV PGDATA=${PGDATA_FOLDER}
 
 FROM lab
 
+# WARNING: If you change this, you have to change it in base-with-services as well
+ENV PGDATA="/home/${NB_USER}/.postgresql"
+
 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_FOLDER} ${PGDATA_FOLDER}
+COPY --from=base ${PGDATA} ${PGDATA}
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "/home/${NB_USER}/.aiida"

From 94ab0411b923f7b5a3d2a37545d053819dbf7947 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 18:50:09 +0100
Subject: [PATCH 25/33] Try thisA

---
 stack/full-stack/Dockerfile | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 2a10f234..a58e8096 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -6,15 +6,13 @@ FROM lab
 # WARNING: If you change this, you have to change it in base-with-services as well
 ENV PGDATA="/home/${NB_USER}/.postgresql"
 
-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"
+#RUN fix-permissions "${CONDA_DIR}"
+#RUN fix-permissions "/home/${NB_USER}/.aiida"
 
 USER ${NB_USER}
 

From ae59bdb161b7afcdffabb195caa21bdf199900f2 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 19:07:56 +0100
Subject: [PATCH 26/33] ?

---
 stack/full-stack/Dockerfile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index a58e8096..be9ed577 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -3,6 +3,8 @@ FROM base-with-services as base
 
 FROM lab
 
+USER root
+
 # WARNING: If you change this, you have to change it in base-with-services as well
 ENV PGDATA="/home/${NB_USER}/.postgresql"
 
@@ -11,8 +13,9 @@ COPY --from=base "${CONDA_DIR}/envs/aiida-core-services" "${CONDA_DIR}/envs/aiid
 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"
+RUN fix-permissions "${CONDA_DIR}"
+RUN fix-permissions "/home/${NB_USER}/.aiida"
+RUN fix-permissions "/home/${NB_USER}/.postgresql"
 
 USER ${NB_USER}
 

From 8378fa50fd67ef06794b4b812451adbd86f1ffb8 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 19:24:26 +0100
Subject: [PATCH 27/33] Sigh

---
 stack/full-stack/Dockerfile | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index be9ed577..997aebe2 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -5,18 +5,15 @@ FROM lab
 
 USER root
 
-# WARNING: If you change this, you have to change it in base-with-services as well
-ENV PGDATA="/home/${NB_USER}/.postgresql"
-
 COPY --from=base /opt/config-quick-setup.yaml /opt/
 COPY --from=base "${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"
-RUN fix-permissions "/home/${NB_USER}/.postgresql"
 
 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"
+COPY --from=base ${PGDATA} ${PGDATA}
 
 WORKDIR "/home/${NB_USER}"

From 236902b80a0ddb95695633ce81e68fbe3239c14f Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 19:37:32 +0100
Subject: [PATCH 28/33] pretty print json output

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 56c5f7f7..39ad0a30 100644
--- a/.github/workflows/build.yml
+++ b/.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}" | jq
               env:
                   BAKE_METADATA: ${{ steps.build-upload.outputs.metadata }}

From 5b2d0bd46a2b1d4d1abfde6b32ade7f3136b8f61 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 19:43:41 +0100
Subject: [PATCH 29/33] Pretty please

---
 stack/full-stack/Dockerfile | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 997aebe2..acde2ce9 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -3,17 +3,18 @@ FROM base-with-services as base
 
 FROM lab
 
+# WARNING: If you change this, you have to change it in base-with-services as well
+ENV PGDATA="/home/${NB_USER}/.postgresql"
 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 "${CONDA_DIR}"
 RUN fix-permissions "${CONDA_DIR}"
 
 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"
-COPY --from=base ${PGDATA} ${PGDATA}
 
 WORKDIR "/home/${NB_USER}"

From 2cfe15a1e0bc076416d8856451e43f4ba04e7e5e Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 19:53:09 +0100
Subject: [PATCH 30/33] hmm

---
 .github/workflows/build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 39ad0a30..8a39a2ea 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -74,6 +74,7 @@ jobs:
             - name: Set output variables
               id: bake_metadata
               run: |
-                  .github/workflows/extract-image-names.sh | tee -a "${GITHUB_OUTPUT}" | jq
+                  .github/workflows/extract-image-names.sh | tee -a "${GITHUB_OUTPUT}"
+                  echo $images | jq
               env:
                   BAKE_METADATA: ${{ steps.build-upload.outputs.metadata }}

From d480087ab0dea9a650a642447948b7a0ecab0296 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 20:07:13 +0100
Subject: [PATCH 31/33] ...

---
 .github/workflows/build.yml | 3 +--
 stack/full-stack/Dockerfile | 3 ++-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 8a39a2ea..bc4ec1e3 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -74,7 +74,6 @@ jobs:
             - name: Set output variables
               id: bake_metadata
               run: |
-                  .github/workflows/extract-image-names.sh | tee -a "${GITHUB_OUTPUT}"
-                  echo $images | jq
+                  .github/workflows/extract-image-names.sh | tee -a "${GITHUB_OUTPUT}" | awk -F'=' '{print $2}' | jq
               env:
                   BAKE_METADATA: ${{ steps.build-upload.outputs.metadata }}
diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index acde2ce9..1266b3a5 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -10,7 +10,8 @@ USER root
 COPY --from=base /opt/config-quick-setup.yaml /opt/
 COPY --from=base "${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} ${PGDATA}
+COPY --from=base "${PGDATA}" "${PGDATA}"
+RUN chown "${NB_USER}" "${PGDATA}"
 
 RUN fix-permissions "${CONDA_DIR}"
 RUN fix-permissions "${CONDA_DIR}"

From daa56eaa626efe62b21e802abd73e7f273ceddc3 Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 20:28:40 +0100
Subject: [PATCH 32/33] Getting closer

---
 stack/full-stack/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 1266b3a5..5035af7f 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -11,10 +11,10 @@ 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 chown "${NB_USER}" "${PGDATA}"
 
 RUN fix-permissions "${CONDA_DIR}"
-RUN fix-permissions "${CONDA_DIR}"
+RUN fix-permissions "/home/${NB_USER}/.aiida"
+RUN chown "${NB_USER}" "${PGDATA}"
 
 USER ${NB_USER}
 

From c08dd3dc759f63dd453bfe593acb226ff2802e4c Mon Sep 17 00:00:00 2001
From: Daniel Hollas <daniel.hollas@bristol.ac.uk>
Date: Sun, 26 May 2024 20:58:06 +0100
Subject: [PATCH 33/33] Screw this

---
 stack/full-stack/Dockerfile | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile
index 5035af7f..61ea23a5 100644
--- a/stack/full-stack/Dockerfile
+++ b/stack/full-stack/Dockerfile
@@ -3,19 +3,21 @@ FROM base-with-services as base
 
 FROM lab
 
-# WARNING: If you change this, you have to change it in base-with-services as well
-ENV PGDATA="/home/${NB_USER}/.postgresql"
 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"
-RUN chown "${NB_USER}" "${PGDATA}"
 
 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}"