From 6399e2c0929e4f1a2d21232bb9c5699f9782428f Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Tue, 2 Mar 2021 12:38:18 +0000
Subject: [PATCH 1/7] Experimental alternative build system

---
 .../ehrbase-postgresql-full-pgw.dockerfile    | 45 +++++++++++++++++++
 dockerfiles/scripts/init-db.sh                | 15 +++++++
 2 files changed, 60 insertions(+)
 create mode 100644 dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
 create mode 100644 dockerfiles/scripts/init-db.sh

diff --git a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
new file mode 100644
index 0000000..b6d1f59
--- /dev/null
+++ b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
@@ -0,0 +1,45 @@
+FROM postgres:11.5-alpine
+
+# Set default values for database user and passwords
+ARG EHRBASE_USER="ehrbase"
+ARG EHRBASE_PASSWORD="ehrbase"
+ENV EHRBASE_USER=${EHRBASE_USER}
+ENV EHRBASE_PASSWORD=${EHRBASE_PASSWORD}
+
+# Set Postgres data directory to custom folder
+ENV PGDATA="/var/lib/postgresql/pgdata"
+
+# Create custom data directory and change ownership to postgres user
+USER root
+RUN mkdir -p ${PGDATA}
+RUN chown postgres: ${PGDATA}
+RUN chmod 0700 ${PGDATA}
+
+# Define Postgres version for easier upgrades for the future
+ENV PG_MAJOR=11.11
+
+# Copy init scripts to init directory
+COPY ./scripts/create-ehrbase-user.sh /docker-entrypoint-initdb.d/
+
+# Initialize basic database cluster
+RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
+    sleep 20 && \
+    echo "Database initialized"
+
+# Allow connections from all adresses & Listen to all interfaces
+RUN echo "host  all  all   0.0.0.0/0  scram-sha-256" >> ${PGDATA}/pg_hba.conf
+RUN echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
+
+# Install python and dependencies
+RUN apk add --update postgresql=${PG_MAJOR}-r0 \
+    build-base  \
+    git         \
+    flex        \
+    bison
+
+COPY scripts /scripts
+RUN chmod +x /scripts/*
+RUN env > /scripts/.env
+RUN sh /scripts/init-db.sh
+
+EXPOSE 5432
diff --git a/dockerfiles/scripts/init-db.sh b/dockerfiles/scripts/init-db.sh
new file mode 100644
index 0000000..63d3e5d
--- /dev/null
+++ b/dockerfiles/scripts/init-db.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# Chjange to the same directory as this script
+cd "$(dirname "$0")"
+
+# Import all env's that was present at the time of init
+set -o allexport
+[[ -f .env ]] && source .env
+set +o allexport
+
+# Execute the DB init scripts
+sh -c "./install-temporal-tables.sh"
+sh -c "./install-jsquery.sh"
+sh -c "./prepare-databases.sh"
+

From c86566d3c537a74d67e32b5f8d56300aceb8e26c Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Tue, 2 Mar 2021 13:39:41 +0000
Subject: [PATCH 2/7] Progressed idea to chainload postgres entrypoint

---
 .../ehrbase-postgresql-full-pgw.dockerfile    |  1 +
 dockerfiles/scripts/create-ehrbase-user.sh    | 18 +++++++----
 dockerfiles/scripts/init-db.sh                | 20 +++++++++++-
 dockerfiles/scripts/install-jsquery.sh        | 17 ++++++----
 .../scripts/install-temporal-tables.sh        | 28 +++++++++-------
 dockerfiles/scripts/prepare-databases.sh      | 32 +++++++++++--------
 6 files changed, 75 insertions(+), 41 deletions(-)

diff --git a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
index b6d1f59..4f140ce 100644
--- a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
+++ b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
@@ -43,3 +43,4 @@ RUN env > /scripts/.env
 RUN sh /scripts/init-db.sh
 
 EXPOSE 5432
+CMD eval /docker-entrypoint.sh
diff --git a/dockerfiles/scripts/create-ehrbase-user.sh b/dockerfiles/scripts/create-ehrbase-user.sh
index 7387a83..adc6ea0 100644
--- a/dockerfiles/scripts/create-ehrbase-user.sh
+++ b/dockerfiles/scripts/create-ehrbase-user.sh
@@ -1,12 +1,16 @@
 #!/bin/bash
 set -e
 
-psql --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
-    CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}';
-    CREATE DATABASE ehrbase ENCODING 'UTF-8' TEMPLATE template0;
-    GRANT ALL PRIVILEGES ON DATABASE ehrbase TO ${EHRBASE_USER};
-    CREATE USER root WITH SUPERUSER;
+if [ ! -f /var/lib/postgresql/pgdata/.userinit ]; then
+
+    psql --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
+        CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}';
+        CREATE DATABASE ehrbase ENCODING 'UTF-8' TEMPLATE template0;
+        GRANT ALL PRIVILEGES ON DATABASE ehrbase TO ${EHRBASE_USER};
+        CREATE USER root WITH SUPERUSER;
 EOSQL
 
-# Stop database before proceeding
-su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+    # Stop database before proceeding
+    su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+    echo "done" > /var/lib/postgresql/pgdata/.userinit
+fi
diff --git a/dockerfiles/scripts/init-db.sh b/dockerfiles/scripts/init-db.sh
index 63d3e5d..0888771 100644
--- a/dockerfiles/scripts/init-db.sh
+++ b/dockerfiles/scripts/init-db.sh
@@ -1,8 +1,14 @@
-#!/bin/bash
+#!/bin/sh
 
 # Chjange to the same directory as this script
 cd "$(dirname "$0")"
 
+# If we was in build we are in the scripts directory
+# if we booted we are in /
+if [ -d scripts ]; then
+    cd scripts
+fi;
+
 # Import all env's that was present at the time of init
 set -o allexport
 [[ -f .env ]] && source .env
@@ -13,3 +19,15 @@ sh -c "./install-temporal-tables.sh"
 sh -c "./install-jsquery.sh"
 sh -c "./prepare-databases.sh"
 
+# Next we need to swap back to docker root
+cd /
+
+# move the standard docker-entrypoint and replace with our own
+if [ ! -f /docker-entrypoint-primary.sh ]; then
+    unlink /docker-entrypoint.sh
+    ln -s /scripts/init-db.sh /docker-entrypoint.sh
+    ln -s /usr/local/bin/docker-entrypoint.sh /docker-entrypoint-primary.sh
+else
+    echo "exec: /docker-entrypoint-primary.sh";
+    bash docker-entrypoint-primary.sh postgres
+fi
diff --git a/dockerfiles/scripts/install-jsquery.sh b/dockerfiles/scripts/install-jsquery.sh
index 4c7bed3..b7ef1d7 100644
--- a/dockerfiles/scripts/install-jsquery.sh
+++ b/dockerfiles/scripts/install-jsquery.sh
@@ -2,12 +2,15 @@
 
 set -e
 
-# Fetch from remote repository
-git clone https://github.com/postgrespro/jsquery.git
-cd jsquery
+if [ ! -f /var/lib/postgresql/pgdata/.jsquery_installed ]; then
+    # Fetch from remote repository
+    git clone https://github.com/postgrespro/jsquery.git
+    cd jsquery
 
-# Build jsQuery plugin
-make USE_PGXS=1 && \
-make USE_PGXS=1 install && \
+    # Build jsQuery plugin
+    make USE_PGXS=1 && \
+    make USE_PGXS=1 install && \
 
-cd ..
\ No newline at end of file
+    cd ..
+    echo "done" > /var/lib/postgresql/pgdata/.jsquery_installed
+fi
diff --git a/dockerfiles/scripts/install-temporal-tables.sh b/dockerfiles/scripts/install-temporal-tables.sh
index 6314eb4..3b47591 100644
--- a/dockerfiles/scripts/install-temporal-tables.sh
+++ b/dockerfiles/scripts/install-temporal-tables.sh
@@ -2,19 +2,23 @@
 
 set -e
 
-# Start server
-su - postgres -c "pg_ctl -D ${PGDATA} -w start"
+if [ ! -f /var/lib/postgresql/pgdata/.temporary_tables_installed ]; then
+    # Start server
+    su - postgres -c "pg_ctl -D ${PGDATA} -w start"
 
-# Fetch from branch "mlt" which has full support of Postgres 11
-git clone https://github.com/mlt/temporal_tables.git --branch mlt
-cd temporal_tables
+    # Fetch from branch "mlt" which has full support of Postgres 11
+    git clone https://github.com/mlt/temporal_tables.git --branch mlt
+    cd temporal_tables
 
-# Build from source
-make PGUSER=postgres &&
-make install &&
-make installcheck
+    # Build from source
+    make PGUSER=postgres &&
+    make install &&
+    make installcheck
 
-# Stop server
-su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+    # Stop server
+    su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+
+    cd ..
+    echo "done" > /var/lib/postgresql/pgdata/.temporary_tables_installed
+fi
 
-cd ..
\ No newline at end of file
diff --git a/dockerfiles/scripts/prepare-databases.sh b/dockerfiles/scripts/prepare-databases.sh
index c091668..baa17c1 100644
--- a/dockerfiles/scripts/prepare-databases.sh
+++ b/dockerfiles/scripts/prepare-databases.sh
@@ -2,20 +2,24 @@
 
 set -e
 
-# Start server
-su - postgres -c "pg_ctl -D ${PGDATA} -w start"
+if [ ! -f /var/lib/postgresql/pgdata/.prepared_tables ]; then
 
-# Setup schemas and activate extensions
-psql --username="$POSTGRES_USER" --dbname "ehrbase" <<-EOSQL
-  CREATE SCHEMA IF NOT EXISTS ehr AUTHORIZATION "$EHRBASE_USER";
-  CREATE SCHEMA IF NOT EXISTS ext AUTHORIZATION "$EHRBASE_USER";
-  CREATE EXTENSION IF NOT EXISTS "uuid-ossp" SCHEMA ext;
-  CREATE EXTENSION IF NOT EXISTS "temporal_tables" SCHEMA ext;
-  CREATE EXTENSION IF NOT EXISTS "jsquery" SCHEMA ext;
-  CREATE EXTENSION IF NOT EXISTS "ltree" SCHEMA ext;
-  ALTER DATABASE ehrbase SET search_path to "$EHRBASE_USER",public,ext;
-  GRANT ALL ON ALL FUNCTIONS IN SCHEMA ext TO $EHRBASE_USER;
+    # Start server
+    su - postgres -c "pg_ctl -D ${PGDATA} -w start"
+
+    # Setup schemas and activate extensions
+    psql --username="$POSTGRES_USER" --dbname "ehrbase" <<-EOSQL
+      CREATE SCHEMA IF NOT EXISTS ehr AUTHORIZATION "$EHRBASE_USER";
+      CREATE SCHEMA IF NOT EXISTS ext AUTHORIZATION "$EHRBASE_USER";
+      CREATE EXTENSION IF NOT EXISTS "uuid-ossp" SCHEMA ext;
+      CREATE EXTENSION IF NOT EXISTS "temporal_tables" SCHEMA ext;
+      CREATE EXTENSION IF NOT EXISTS "jsquery" SCHEMA ext;
+      CREATE EXTENSION IF NOT EXISTS "ltree" SCHEMA ext;
+      ALTER DATABASE ehrbase SET search_path to "$EHRBASE_USER",public,ext;
+      GRANT ALL ON ALL FUNCTIONS IN SCHEMA ext TO $EHRBASE_USER;
 EOSQL
 
-# Stop server
-su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+    # Stop server
+    su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+    echo "done" > /var/lib/postgresql/pgdata/.prepared_tables
+fi

From 4ef181b512e4b48c2aa2bd78a845ab5d71342dea Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Tue, 2 Mar 2021 13:48:53 +0000
Subject: [PATCH 3/7] Experimental working build

---
 dockerfiles/ehrbase-postgresql-full-pgw.dockerfile | 3 ++-
 dockerfiles/scripts/init-db.sh                     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
index 4f140ce..4063c3b 100644
--- a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
+++ b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
@@ -43,4 +43,5 @@ RUN env > /scripts/.env
 RUN sh /scripts/init-db.sh
 
 EXPOSE 5432
-CMD eval /docker-entrypoint.sh
+
+ENTRYPOINT ["/docker-entrypoint.sh"]
diff --git a/dockerfiles/scripts/init-db.sh b/dockerfiles/scripts/init-db.sh
index 0888771..6bede56 100644
--- a/dockerfiles/scripts/init-db.sh
+++ b/dockerfiles/scripts/init-db.sh
@@ -29,5 +29,5 @@ if [ ! -f /docker-entrypoint-primary.sh ]; then
     ln -s /usr/local/bin/docker-entrypoint.sh /docker-entrypoint-primary.sh
 else
     echo "exec: /docker-entrypoint-primary.sh";
-    bash docker-entrypoint-primary.sh postgres
+    ./docker-entrypoint-primary.sh postgres
 fi

From 761dbb6b8ac97d1353e304a02a9c9a486daa4fab Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Tue, 2 Mar 2021 16:16:50 +0000
Subject: [PATCH 4/7] Working I believe

---
 .../ehrbase-postgresql-full-pgw.dockerfile    | 43 +++++++++++--------
 dockerfiles/scripts/chain-load.sh             | 30 +++++++++++++
 dockerfiles/scripts/create-ehrbase-user.sh    | 19 ++++----
 dockerfiles/scripts/init-db.sh                | 33 --------------
 .../scripts/install-temporal-tables.sh        | 24 ++++-------
 dockerfiles/scripts/prepare-databases.sh      | 35 +++++++--------
 6 files changed, 92 insertions(+), 92 deletions(-)
 create mode 100644 dockerfiles/scripts/chain-load.sh
 delete mode 100644 dockerfiles/scripts/init-db.sh

diff --git a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
index 4063c3b..f43b7f0 100644
--- a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
+++ b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
@@ -11,24 +11,31 @@ ENV PGDATA="/var/lib/postgresql/pgdata"
 
 # Create custom data directory and change ownership to postgres user
 USER root
-RUN mkdir -p ${PGDATA}
+RUN mkdir -p ${PGDATA} /usr/local/share/doc/
 RUN chown postgres: ${PGDATA}
 RUN chmod 0700 ${PGDATA}
 
 # Define Postgres version for easier upgrades for the future
 ENV PG_MAJOR=11.11
 
-# Copy init scripts to init directory
-COPY ./scripts/create-ehrbase-user.sh /docker-entrypoint-initdb.d/
-
-# Initialize basic database cluster
-RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
-    sleep 20 && \
-    echo "Database initialized"
+# Copy system scripts to the scripts directory on root
+COPY scripts /scripts
+RUN chmod +x /scripts/*
+RUN env > /scripts/.env
 
-# Allow connections from all adresses & Listen to all interfaces
-RUN echo "host  all  all   0.0.0.0/0  scram-sha-256" >> ${PGDATA}/pg_hba.conf
-RUN echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
+# Copy init scripts to init directory
+COPY ./scripts/chain-load.sh /docker-entrypoint-initdb.d/
+RUN chown -R root:postgres  /scripts                                \
+                            /usr/local/lib/postgresql               \
+                            /usr/local/include/postgresql           \
+                            /usr/local/share/postgresql/extension   \
+                            /usr/local/share/doc/
+
+RUN chmod -R g+rwx          /scripts                                \
+                            /usr/local/lib/postgresql               \
+                            /usr/local/include/postgresql           \
+                            /usr/local/share/postgresql/extension   \
+                            /usr/local/share/doc/
 
 # Install python and dependencies
 RUN apk add --update postgresql=${PG_MAJOR}-r0 \
@@ -37,11 +44,13 @@ RUN apk add --update postgresql=${PG_MAJOR}-r0 \
     flex        \
     bison
 
-COPY scripts /scripts
-RUN chmod +x /scripts/*
-RUN env > /scripts/.env
-RUN sh /scripts/init-db.sh
+# Initialize basic database cluster
+RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
+    sleep 20 && \
+    echo "Database initialized"
 
-EXPOSE 5432
+# Allow connections from all adresses & Listen to all interfaces
+RUN echo "host  all  all   0.0.0.0/0  md5" >> ${PGDATA}/pg_hba.conf
+RUN echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
 
-ENTRYPOINT ["/docker-entrypoint.sh"]
+EXPOSE 5432
diff --git a/dockerfiles/scripts/chain-load.sh b/dockerfiles/scripts/chain-load.sh
new file mode 100644
index 0000000..bef60cd
--- /dev/null
+++ b/dockerfiles/scripts/chain-load.sh
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+set -e
+
+cd /scripts
+
+set -o allexport
+[[ -f .env ]] && source .env
+set +o allexport
+
+# Check if it is already initilized
+if [ -f /var/lib/postgresql/pgdata/.prepared ]; then
+    echo "Database has already been initilized"
+else
+    # Execute the DB init scripts
+    echo "Running: create-ehrbase-user"
+    eval ./create-ehrbase-user.sh
+
+    echo "Installing temporal tables"
+    rm -Rf temporal*
+    eval ./install-temporal-tables.sh
+
+    echo "Installing JSquery"
+    rm -Rf jsquery*
+    eval ./install-jsquery.sh
+
+    echo "Creating default databases"
+    eval ./prepare-databases.sh
+fi
+
diff --git a/dockerfiles/scripts/create-ehrbase-user.sh b/dockerfiles/scripts/create-ehrbase-user.sh
index adc6ea0..2461878 100644
--- a/dockerfiles/scripts/create-ehrbase-user.sh
+++ b/dockerfiles/scripts/create-ehrbase-user.sh
@@ -1,16 +1,15 @@
 #!/bin/bash
 set -e
 
-if [ ! -f /var/lib/postgresql/pgdata/.userinit ]; then
+echo "CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}'"
 
-    psql --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
-        CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}';
-        CREATE DATABASE ehrbase ENCODING 'UTF-8' TEMPLATE template0;
-        GRANT ALL PRIVILEGES ON DATABASE ehrbase TO ${EHRBASE_USER};
-        CREATE USER root WITH SUPERUSER;
+psql --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
+CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}';
+CREATE DATABASE ehrbase ENCODING 'UTF-8' TEMPLATE template0;
+GRANT ALL PRIVILEGES ON DATABASE ehrbase TO ${EHRBASE_USER};
+CREATE USER root WITH SUPERUSER;
 EOSQL
 
-    # Stop database before proceeding
-    su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
-    echo "done" > /var/lib/postgresql/pgdata/.userinit
-fi
+# Stop database before proceeding
+pg_ctl stop -D ${PGDATA}
+echo "done" > /var/lib/postgresql/pgdata/.userinit
diff --git a/dockerfiles/scripts/init-db.sh b/dockerfiles/scripts/init-db.sh
deleted file mode 100644
index 6bede56..0000000
--- a/dockerfiles/scripts/init-db.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh
-
-# Chjange to the same directory as this script
-cd "$(dirname "$0")"
-
-# If we was in build we are in the scripts directory
-# if we booted we are in /
-if [ -d scripts ]; then
-    cd scripts
-fi;
-
-# Import all env's that was present at the time of init
-set -o allexport
-[[ -f .env ]] && source .env
-set +o allexport
-
-# Execute the DB init scripts
-sh -c "./install-temporal-tables.sh"
-sh -c "./install-jsquery.sh"
-sh -c "./prepare-databases.sh"
-
-# Next we need to swap back to docker root
-cd /
-
-# move the standard docker-entrypoint and replace with our own
-if [ ! -f /docker-entrypoint-primary.sh ]; then
-    unlink /docker-entrypoint.sh
-    ln -s /scripts/init-db.sh /docker-entrypoint.sh
-    ln -s /usr/local/bin/docker-entrypoint.sh /docker-entrypoint-primary.sh
-else
-    echo "exec: /docker-entrypoint-primary.sh";
-    ./docker-entrypoint-primary.sh postgres
-fi
diff --git a/dockerfiles/scripts/install-temporal-tables.sh b/dockerfiles/scripts/install-temporal-tables.sh
index 3b47591..02404ff 100644
--- a/dockerfiles/scripts/install-temporal-tables.sh
+++ b/dockerfiles/scripts/install-temporal-tables.sh
@@ -2,23 +2,17 @@
 
 set -e
 
-if [ ! -f /var/lib/postgresql/pgdata/.temporary_tables_installed ]; then
-    # Start server
-    su - postgres -c "pg_ctl -D ${PGDATA} -w start"
+pg_ctl start -D ${PGDATA} 
 
-    # Fetch from branch "mlt" which has full support of Postgres 11
-    git clone https://github.com/mlt/temporal_tables.git --branch mlt
-    cd temporal_tables
+# Fetch from branch "mlt" which has full support of Postgres 11
+git clone https://github.com/mlt/temporal_tables.git --branch mlt
+cd temporal_tables
 
-    # Build from source
-    make PGUSER=postgres &&
-    make install &&
-    make installcheck
+# Build from source
+make PGUSER=postgres && make install && make installcheck
 
-    # Stop server
-    su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+# Stop server
+pg_ctl stop -D ${PGDATA}
 
-    cd ..
-    echo "done" > /var/lib/postgresql/pgdata/.temporary_tables_installed
-fi
+cd ..
 
diff --git a/dockerfiles/scripts/prepare-databases.sh b/dockerfiles/scripts/prepare-databases.sh
index baa17c1..d232e8e 100644
--- a/dockerfiles/scripts/prepare-databases.sh
+++ b/dockerfiles/scripts/prepare-databases.sh
@@ -2,24 +2,25 @@
 
 set -e
 
-if [ ! -f /var/lib/postgresql/pgdata/.prepared_tables ]; then
 
-    # Start server
-    su - postgres -c "pg_ctl -D ${PGDATA} -w start"
+# Start server
+pg_ctl start -D ${PGDATA}
 
-    # Setup schemas and activate extensions
-    psql --username="$POSTGRES_USER" --dbname "ehrbase" <<-EOSQL
-      CREATE SCHEMA IF NOT EXISTS ehr AUTHORIZATION "$EHRBASE_USER";
-      CREATE SCHEMA IF NOT EXISTS ext AUTHORIZATION "$EHRBASE_USER";
-      CREATE EXTENSION IF NOT EXISTS "uuid-ossp" SCHEMA ext;
-      CREATE EXTENSION IF NOT EXISTS "temporal_tables" SCHEMA ext;
-      CREATE EXTENSION IF NOT EXISTS "jsquery" SCHEMA ext;
-      CREATE EXTENSION IF NOT EXISTS "ltree" SCHEMA ext;
-      ALTER DATABASE ehrbase SET search_path to "$EHRBASE_USER",public,ext;
-      GRANT ALL ON ALL FUNCTIONS IN SCHEMA ext TO $EHRBASE_USER;
+echo "Creating schemas"
+
+# Setup schemas and activate extensions
+psql --username="$POSTGRES_USER" --dbname "ehrbase" <<-EOSQL
+CREATE SCHEMA IF NOT EXISTS ehr AUTHORIZATION "$EHRBASE_USER";
+CREATE SCHEMA IF NOT EXISTS ext AUTHORIZATION "$EHRBASE_USER";
+CREATE EXTENSION IF NOT EXISTS "uuid-ossp" SCHEMA ext;
+CREATE EXTENSION IF NOT EXISTS "temporal_tables" SCHEMA ext;
+CREATE EXTENSION IF NOT EXISTS "jsquery" SCHEMA ext;
+CREATE EXTENSION IF NOT EXISTS "ltree" SCHEMA ext;
+ALTER DATABASE ehrbase SET search_path to "$EHRBASE_USER",public,ext;
+GRANT ALL ON ALL FUNCTIONS IN SCHEMA ext TO $EHRBASE_USER;
 EOSQL
 
-    # Stop server
-    su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
-    echo "done" > /var/lib/postgresql/pgdata/.prepared_tables
-fi
+# Stop server
+pg_ctl stop -D ${PGDATA}
+
+echo "done" > /var/lib/postgresql/pgdata/.prepared

From 331624b100117124a69e4d7415c64bf63cf961c7 Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Tue, 2 Mar 2021 16:20:16 +0000
Subject: [PATCH 5/7] Overwrote original dockerfile for pull request sanity

---
 .../ehrbase-postgresql-full-pgw.dockerfile    | 56 ------------------
 .../ehrbase-postgresql-full.dockerfile        | 58 +++++++++----------
 2 files changed, 28 insertions(+), 86 deletions(-)
 delete mode 100644 dockerfiles/ehrbase-postgresql-full-pgw.dockerfile

diff --git a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile b/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
deleted file mode 100644
index f43b7f0..0000000
--- a/dockerfiles/ehrbase-postgresql-full-pgw.dockerfile
+++ /dev/null
@@ -1,56 +0,0 @@
-FROM postgres:11.5-alpine
-
-# Set default values for database user and passwords
-ARG EHRBASE_USER="ehrbase"
-ARG EHRBASE_PASSWORD="ehrbase"
-ENV EHRBASE_USER=${EHRBASE_USER}
-ENV EHRBASE_PASSWORD=${EHRBASE_PASSWORD}
-
-# Set Postgres data directory to custom folder
-ENV PGDATA="/var/lib/postgresql/pgdata"
-
-# Create custom data directory and change ownership to postgres user
-USER root
-RUN mkdir -p ${PGDATA} /usr/local/share/doc/
-RUN chown postgres: ${PGDATA}
-RUN chmod 0700 ${PGDATA}
-
-# Define Postgres version for easier upgrades for the future
-ENV PG_MAJOR=11.11
-
-# Copy system scripts to the scripts directory on root
-COPY scripts /scripts
-RUN chmod +x /scripts/*
-RUN env > /scripts/.env
-
-# Copy init scripts to init directory
-COPY ./scripts/chain-load.sh /docker-entrypoint-initdb.d/
-RUN chown -R root:postgres  /scripts                                \
-                            /usr/local/lib/postgresql               \
-                            /usr/local/include/postgresql           \
-                            /usr/local/share/postgresql/extension   \
-                            /usr/local/share/doc/
-
-RUN chmod -R g+rwx          /scripts                                \
-                            /usr/local/lib/postgresql               \
-                            /usr/local/include/postgresql           \
-                            /usr/local/share/postgresql/extension   \
-                            /usr/local/share/doc/
-
-# Install python and dependencies
-RUN apk add --update postgresql=${PG_MAJOR}-r0 \
-    build-base  \
-    git         \
-    flex        \
-    bison
-
-# Initialize basic database cluster
-RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
-    sleep 20 && \
-    echo "Database initialized"
-
-# Allow connections from all adresses & Listen to all interfaces
-RUN echo "host  all  all   0.0.0.0/0  md5" >> ${PGDATA}/pg_hba.conf
-RUN echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
-
-EXPOSE 5432
diff --git a/dockerfiles/ehrbase-postgresql-full.dockerfile b/dockerfiles/ehrbase-postgresql-full.dockerfile
index 75b2530..f43b7f0 100644
--- a/dockerfiles/ehrbase-postgresql-full.dockerfile
+++ b/dockerfiles/ehrbase-postgresql-full.dockerfile
@@ -10,15 +10,39 @@ ENV EHRBASE_PASSWORD=${EHRBASE_PASSWORD}
 ENV PGDATA="/var/lib/postgresql/pgdata"
 
 # Create custom data directory and change ownership to postgres user
-RUN mkdir -p ${PGDATA}
+USER root
+RUN mkdir -p ${PGDATA} /usr/local/share/doc/
 RUN chown postgres: ${PGDATA}
 RUN chmod 0700 ${PGDATA}
 
 # Define Postgres version for easier upgrades for the future
-ENV PG_MAJOR=11.10
+ENV PG_MAJOR=11.11
+
+# Copy system scripts to the scripts directory on root
+COPY scripts /scripts
+RUN chmod +x /scripts/*
+RUN env > /scripts/.env
 
 # Copy init scripts to init directory
-COPY ./scripts/create-ehrbase-user.sh /docker-entrypoint-initdb.d/
+COPY ./scripts/chain-load.sh /docker-entrypoint-initdb.d/
+RUN chown -R root:postgres  /scripts                                \
+                            /usr/local/lib/postgresql               \
+                            /usr/local/include/postgresql           \
+                            /usr/local/share/postgresql/extension   \
+                            /usr/local/share/doc/
+
+RUN chmod -R g+rwx          /scripts                                \
+                            /usr/local/lib/postgresql               \
+                            /usr/local/include/postgresql           \
+                            /usr/local/share/postgresql/extension   \
+                            /usr/local/share/doc/
+
+# Install python and dependencies
+RUN apk add --update postgresql=${PG_MAJOR}-r0 \
+    build-base  \
+    git         \
+    flex        \
+    bison
 
 # Initialize basic database cluster
 RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
@@ -26,33 +50,7 @@ RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
     echo "Database initialized"
 
 # Allow connections from all adresses & Listen to all interfaces
-RUN echo "host  all  all   0.0.0.0/0  scram-sha-256" >> ${PGDATA}/pg_hba.conf
+RUN echo "host  all  all   0.0.0.0/0  md5" >> ${PGDATA}/pg_hba.conf
 RUN echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
 
-# Install python and dependencies
-RUN apk add --update postgresql=${PG_MAJOR}-r0 \
-    build-base \
-    git \
-    flex \
-    bison
-
-# Install temporary_tables plugin
-COPY ./scripts/install-temporal-tables.sh .
-RUN chmod +x ./install-temporal-tables.sh
-RUN sh -c "./install-temporal-tables.sh"
-
-# Install jsquery plugin
-COPY ./scripts/install-jsquery.sh .
-RUN chmod +x ./install-jsquery.sh 
-RUN sh -c "./install-jsquery.sh"
-
-# Prepare database schemas
-COPY ./scripts/prepare-databases.sh .
-RUN chmod +x ./prepare-databases.sh
-RUN sh -c "./prepare-databases.sh"
-
-# Cleanup
-RUN rm -f -r ./jsquery
-RUN rm -f -r ./temporal_tables
-
 EXPOSE 5432

From 1c70e35100a754da47d4ed07e8490896fd24f212 Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Wed, 3 Mar 2021 20:43:22 +0000
Subject: [PATCH 6/7] Rather large refactor

---
 .../ehrbase-postgresql-full.dockerfile        | 58 ++++++-----
 dockerfiles/scripts/chain-load.sh             | 68 +++++++++----
 dockerfiles/scripts/create-ehrbase-user.sh    | 11 +--
 dockerfiles/scripts/etc/pg_hba.conf           | 95 +++++++++++++++++++
 dockerfiles/scripts/install-jsquery.sh        | 16 ----
 .../scripts/install-temporal-tables.sh        | 18 ----
 dockerfiles/scripts/prepare-databases.sh      | 11 ---
 dockerfiles/scripts/test-temporal-tables.sh   |  6 ++
 8 files changed, 187 insertions(+), 96 deletions(-)
 create mode 100644 dockerfiles/scripts/etc/pg_hba.conf
 delete mode 100644 dockerfiles/scripts/install-jsquery.sh
 delete mode 100644 dockerfiles/scripts/install-temporal-tables.sh
 create mode 100644 dockerfiles/scripts/test-temporal-tables.sh

diff --git a/dockerfiles/ehrbase-postgresql-full.dockerfile b/dockerfiles/ehrbase-postgresql-full.dockerfile
index f43b7f0..de48074 100644
--- a/dockerfiles/ehrbase-postgresql-full.dockerfile
+++ b/dockerfiles/ehrbase-postgresql-full.dockerfile
@@ -3,8 +3,8 @@ FROM postgres:11.5-alpine
 # Set default values for database user and passwords
 ARG EHRBASE_USER="ehrbase"
 ARG EHRBASE_PASSWORD="ehrbase"
-ENV EHRBASE_USER=${EHRBASE_USER}
-ENV EHRBASE_PASSWORD=${EHRBASE_PASSWORD}
+ENV EHRBASE_USER=${EHRBASE_USER:-ehrbase}
+ENV EHRBASE_PASSWORD=${EHRBASE_PASSWORD:-ehrbase}
 
 # Set Postgres data directory to custom folder
 ENV PGDATA="/var/lib/postgresql/pgdata"
@@ -21,36 +21,46 @@ ENV PG_MAJOR=11.11
 # Copy system scripts to the scripts directory on root
 COPY scripts /scripts
 RUN chmod +x /scripts/*
-RUN env > /scripts/.env
-
-# Copy init scripts to init directory
-COPY ./scripts/chain-load.sh /docker-entrypoint-initdb.d/
-RUN chown -R root:postgres  /scripts                                \
-                            /usr/local/lib/postgresql               \
-                            /usr/local/include/postgresql           \
-                            /usr/local/share/postgresql/extension   \
-                            /usr/local/share/doc/
-
-RUN chmod -R g+rwx          /scripts                                \
-                            /usr/local/lib/postgresql               \
-                            /usr/local/include/postgresql           \
-                            /usr/local/share/postgresql/extension   \
-                            /usr/local/share/doc/
 
 # Install python and dependencies
 RUN apk add --update postgresql=${PG_MAJOR}-r0 \
     build-base  \
     git         \
     flex        \
-    bison
+    bison       \
+    psutils
+
+# Install JSQuery
+RUN cd  /scripts/                                                           \
+    &&  git clone https://github.com/postgrespro/jsquery.git                \
+    &&  cd jsquery                                                          \
+    &&  make USE_PGXS=1                                                     \
+    &&  make USE_PGXS=1 install
+
+# Install temporal tables 
+RUN cd  /scripts/                                                           \
+    &&  git clone https://github.com/mlt/temporal_tables.git --branch mlt   \
+    &&  cd temporal_tables                                                  \
+    &&  make PGUSER=postgres                                                \
+    &&  make install
+
+# Allow regression test to run from /scripts/temporal
+RUN chown -R root:postgres  /scripts
+RUN chmod -R g+rwx          /scripts
 
 # Initialize basic database cluster
-RUN sh -c "/usr/local/bin/docker-entrypoint.sh postgres & " && \
-    sleep 20 && \
-    echo "Database initialized"
+RUN su postgres -c sh -c "/scripts/chain-load.sh SETUP"         \
+    &&  su postgres -c sh -c "/usr/local/bin/docker-entrypoint.sh postgres &"   \
+    &&  su postgres -c sh -c "/scripts/chain-load.sh WAIT"       \
+    &&  su postgres -c sh -c "/scripts/chain-load.sh SPAWNSET"   \
+    &&  su postgres -c sh -c "/scripts/chain-load.sh STOP"
+
+RUN echo "DONE" > /scripts/.pginit
 
-# Allow connections from all adresses & Listen to all interfaces
-RUN echo "host  all  all   0.0.0.0/0  md5" >> ${PGDATA}/pg_hba.conf
-RUN echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
+# Copy init scripts to init directory
+COPY /scripts/chain-load.sh /docker-entrypoint-initdb.d/
+# COPY the pg_hba to the PGDATA directory
+COPY /scripts/etc/pg_hba.conf ${PGDATA}/
+RUN chown -Rv postgres:postgres ${PGDATA}
 
 EXPOSE 5432
diff --git a/dockerfiles/scripts/chain-load.sh b/dockerfiles/scripts/chain-load.sh
index bef60cd..0520c4f 100644
--- a/dockerfiles/scripts/chain-load.sh
+++ b/dockerfiles/scripts/chain-load.sh
@@ -1,30 +1,60 @@
-#!/bin/sh
+#!/bin/bash
 
-set -e
+# Read in ARG0
+STARTSERVER="$1";
 
+# Always swap to /scripts
 cd /scripts
 
-set -o allexport
-[[ -f .env ]] && source .env
-set +o allexport
+# Always expand the enviroment
+set -e
+
+# Incase this is a volume mount move
+if [ -f "/scripts/.pginit" ]; then
+    STARTSERVER="SPAWNSET"
+fi
 
-# Check if it is already initilized
-if [ -f /var/lib/postgresql/pgdata/.prepared ]; then
-    echo "Database has already been initilized"
+if [[ -z "$STARTSERVER" ]]; then
+    echo "No runmode specified!"
+    exit 0
 else
-    # Execute the DB init scripts
-    echo "Running: create-ehrbase-user"
-    eval ./create-ehrbase-user.sh
+    echo "Running mode: $STARTSERVER"
+fi
 
-    echo "Installing temporal tables"
-    rm -Rf temporal*
-    eval ./install-temporal-tables.sh
+# If we are in setup, init the db and install the required databases
+# and modules
+if [ $STARTSERVER == "INIT" ]; then
+    sh -c 'pg_ctl initdb -D ${PGDATA}'
+elif [ "$STARTSERVER" == "START" ]; then
+    sh -c 'pg_ctl start -D ${PGDATA}'
+elif [ "$STARTSERVER" == "WAIT" ]; then
+    LOOPRUN=0
+    while [ "$LOOPRUN" != 1 ]; do
+        sleep 1
+        LOOPRUN=$(perl -e 'print `psql -AtXq -U postgres -d template1 -c "SELECT 1"`')
+    done
+    echo "Primary database initilization complete!"
+elif [ "$STARTSERVER" == "STOP" ]; then
+    sh -c 'pg_ctl stop -D ${PGDATA}'
+elif [ "$STARTSERVER" == "SETUP" ]; then
+    # Totally remove the PGDATA to force re-init on image start
+    rm -Rf "${PGDATA}"
+elif [ "$STARTSERVER" == "SPAWNSET" ]; then
+    # Execute the DB init scripts, we are already the postgres user
+    # Add in MD5 auth
+    echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
+
+    echo "Running temporal table test"
+    eval ./test-temporal-tables.sh
 
-    echo "Installing JSquery"
-    rm -Rf jsquery*
-    eval ./install-jsquery.sh
+    echo "Running: create-ehrbase-user"
+    eval ./create-ehrbase-user.sh
 
     echo "Creating default databases"
     eval ./prepare-databases.sh
-fi
-
+elif [ "$STARTSERVER" == "PASSRESET" ]; then
+    echo "Running: password-recrypt-set"
+    eval ./password-recrypt-set.sh
+else
+    echo "Unknown action '$STARTSERVER' called."
+fi;
diff --git a/dockerfiles/scripts/create-ehrbase-user.sh b/dockerfiles/scripts/create-ehrbase-user.sh
index 2461878..bd874ea 100644
--- a/dockerfiles/scripts/create-ehrbase-user.sh
+++ b/dockerfiles/scripts/create-ehrbase-user.sh
@@ -1,15 +1,10 @@
 #!/bin/bash
-set -e
 
-echo "CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}'"
+echo "Creating user(${EHRBASE_USER}) pass(${EHRBASE_PASSWORD}) db(ehrbase)"
 
-psql --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
-CREATE ROLE ${EHRBASE_USER} LOGIN PASSWORD '${EHRBASE_PASSWORD}';
+psql -U "${POSTGRES_USER}" -d "${POSTGRES_DB}" <<-EOSQL
+CREATE ROLE ${EHRBASE_USER} WITH LOGIN PASSWORD '${EHRBASE_PASSWORD}';
 CREATE DATABASE ehrbase ENCODING 'UTF-8' TEMPLATE template0;
 GRANT ALL PRIVILEGES ON DATABASE ehrbase TO ${EHRBASE_USER};
 CREATE USER root WITH SUPERUSER;
 EOSQL
-
-# Stop database before proceeding
-pg_ctl stop -D ${PGDATA}
-echo "done" > /var/lib/postgresql/pgdata/.userinit
diff --git a/dockerfiles/scripts/etc/pg_hba.conf b/dockerfiles/scripts/etc/pg_hba.conf
new file mode 100644
index 0000000..65bbc2c
--- /dev/null
+++ b/dockerfiles/scripts/etc/pg_hba.conf
@@ -0,0 +1,95 @@
+# PostgreSQL Client Authentication Configuration File
+# ===================================================
+#
+# Refer to the "Client Authentication" section in the PostgreSQL
+# documentation for a complete description of this file.  A short
+# synopsis follows.
+#
+# This file controls: which hosts are allowed to connect, how clients
+# are authenticated, which PostgreSQL user names they can use, which
+# databases they can access.  Records take one of these forms:
+#
+# local      DATABASE  USER  METHOD  [OPTIONS]
+# host       DATABASE  USER  ADDRESS  METHOD  [OPTIONS]
+# hostssl    DATABASE  USER  ADDRESS  METHOD  [OPTIONS]
+# hostnossl  DATABASE  USER  ADDRESS  METHOD  [OPTIONS]
+#
+# (The uppercase items must be replaced by actual values.)
+#
+# The first field is the connection type: "local" is a Unix-domain
+# socket, "host" is either a plain or SSL-encrypted TCP/IP socket,
+# "hostssl" is an SSL-encrypted TCP/IP socket, and "hostnossl" is a
+# plain TCP/IP socket.
+#
+# DATABASE can be "all", "sameuser", "samerole", "replication", a
+# database name, or a comma-separated list thereof. The "all"
+# keyword does not match "replication". Access to replication
+# must be enabled in a separate record (see example below).
+#
+# USER can be "all", a user name, a group name prefixed with "+", or a
+# comma-separated list thereof.  In both the DATABASE and USER fields
+# you can also write a file name prefixed with "@" to include names
+# from a separate file.
+#
+# ADDRESS specifies the set of hosts the record matches.  It can be a
+# host name, or it is made up of an IP address and a CIDR mask that is
+# an integer (between 0 and 32 (IPv4) or 128 (IPv6) inclusive) that
+# specifies the number of significant bits in the mask.  A host name
+# that starts with a dot (.) matches a suffix of the actual host name.
+# Alternatively, you can write an IP address and netmask in separate
+# columns to specify the set of hosts.  Instead of a CIDR-address, you
+# can write "samehost" to match any of the server's own IP addresses,
+# or "samenet" to match any address in any subnet that the server is
+# directly connected to.
+#
+# METHOD can be "trust", "reject", "md5", "password", "scram-sha-256",
+# "gss", "sspi", "ident", "peer", "pam", "ldap", "radius" or "cert".
+# Note that "password" sends passwords in clear text; "md5" or
+# "scram-sha-256" are preferred since they send encrypted passwords.
+#
+# OPTIONS are a set of options for the authentication in the format
+# NAME=VALUE.  The available options depend on the different
+# authentication methods -- refer to the "Client Authentication"
+# section in the documentation for a list of which options are
+# available for which authentication methods.
+#
+# Database and user names containing spaces, commas, quotes and other
+# special characters must be quoted.  Quoting one of the keywords
+# "all", "sameuser", "samerole" or "replication" makes the name lose
+# its special character, and just match a database or username with
+# that name.
+#
+# This file is read on server startup and when the server receives a
+# SIGHUP signal.  If you edit the file on a running system, you have to
+# SIGHUP the server for the changes to take effect, run "pg_ctl reload",
+# or execute "SELECT pg_reload_conf()".
+#
+# Put your actual configuration here
+# ----------------------------------
+#
+# If you want to allow non-local connections, you need to add more
+# "host" records.  In that case you will also need to make PostgreSQL
+# listen on a non-local interface via the listen_addresses
+# configuration parameter, or via the -i or -h command line switches.
+
+# CAUTION: Configuring the system for local "trust" authentication
+# allows any local user to connect as any PostgreSQL user, including
+# the database superuser.  If you do not trust all your local users,
+# use another authentication method.
+
+
+# TYPE  DATABASE        USER            ADDRESS                 METHOD
+
+# "local" is for Unix domain socket connections only
+local   all             all                                     trust
+# IPv4 local connections:
+host    all             all             127.0.0.1/32            trust
+# IPv6 local connections:
+host    all             all             ::1/128                 trust
+# Allow replication connections from localhost, by a user with the
+# replication privilege.
+local   replication     all                                     trust
+host    replication     all             127.0.0.1/32            trust
+host    replication     all             ::1/128                 trust
+# Require MD5 auth for all other connections
+host    all             all             0.0.0.0/0               md5
diff --git a/dockerfiles/scripts/install-jsquery.sh b/dockerfiles/scripts/install-jsquery.sh
deleted file mode 100644
index b7ef1d7..0000000
--- a/dockerfiles/scripts/install-jsquery.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-set -e
-
-if [ ! -f /var/lib/postgresql/pgdata/.jsquery_installed ]; then
-    # Fetch from remote repository
-    git clone https://github.com/postgrespro/jsquery.git
-    cd jsquery
-
-    # Build jsQuery plugin
-    make USE_PGXS=1 && \
-    make USE_PGXS=1 install && \
-
-    cd ..
-    echo "done" > /var/lib/postgresql/pgdata/.jsquery_installed
-fi
diff --git a/dockerfiles/scripts/install-temporal-tables.sh b/dockerfiles/scripts/install-temporal-tables.sh
deleted file mode 100644
index 02404ff..0000000
--- a/dockerfiles/scripts/install-temporal-tables.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-set -e
-
-pg_ctl start -D ${PGDATA} 
-
-# Fetch from branch "mlt" which has full support of Postgres 11
-git clone https://github.com/mlt/temporal_tables.git --branch mlt
-cd temporal_tables
-
-# Build from source
-make PGUSER=postgres && make install && make installcheck
-
-# Stop server
-pg_ctl stop -D ${PGDATA}
-
-cd ..
-
diff --git a/dockerfiles/scripts/prepare-databases.sh b/dockerfiles/scripts/prepare-databases.sh
index d232e8e..cb02c4c 100644
--- a/dockerfiles/scripts/prepare-databases.sh
+++ b/dockerfiles/scripts/prepare-databases.sh
@@ -1,11 +1,5 @@
 #!/bin/bash
 
-set -e
-
-
-# Start server
-pg_ctl start -D ${PGDATA}
-
 echo "Creating schemas"
 
 # Setup schemas and activate extensions
@@ -19,8 +13,3 @@ CREATE EXTENSION IF NOT EXISTS "ltree" SCHEMA ext;
 ALTER DATABASE ehrbase SET search_path to "$EHRBASE_USER",public,ext;
 GRANT ALL ON ALL FUNCTIONS IN SCHEMA ext TO $EHRBASE_USER;
 EOSQL
-
-# Stop server
-pg_ctl stop -D ${PGDATA}
-
-echo "done" > /var/lib/postgresql/pgdata/.prepared
diff --git a/dockerfiles/scripts/test-temporal-tables.sh b/dockerfiles/scripts/test-temporal-tables.sh
new file mode 100644
index 0000000..8688e05
--- /dev/null
+++ b/dockerfiles/scripts/test-temporal-tables.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd /scripts/temporal_tables
+
+# Build from source
+make installcheck

From 8f5c7579f92a21deeb3f8f0acca1f30d95320ad5 Mon Sep 17 00:00:00 2001
From: Paul G Webster <paul.g.webster@googlemail.com>
Date: Wed, 3 Mar 2021 21:02:33 +0000
Subject: [PATCH 7/7] Force refresh of server credentials on re init

---
 dockerfiles/ehrbase-postgresql-full.dockerfile |  3 ++-
 dockerfiles/scripts/chain-load.sh              | 11 +++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/dockerfiles/ehrbase-postgresql-full.dockerfile b/dockerfiles/ehrbase-postgresql-full.dockerfile
index de48074..82ceb53 100644
--- a/dockerfiles/ehrbase-postgresql-full.dockerfile
+++ b/dockerfiles/ehrbase-postgresql-full.dockerfile
@@ -61,6 +61,7 @@ RUN echo "DONE" > /scripts/.pginit
 COPY /scripts/chain-load.sh /docker-entrypoint-initdb.d/
 # COPY the pg_hba to the PGDATA directory
 COPY /scripts/etc/pg_hba.conf ${PGDATA}/
-RUN chown -Rv postgres:postgres ${PGDATA}
+RUN echo "Enforcing ownership, one moment" \
+    && chown -R postgres:postgres ${PGDATA}
 
 EXPOSE 5432
diff --git a/dockerfiles/scripts/chain-load.sh b/dockerfiles/scripts/chain-load.sh
index 0520c4f..98e96c3 100644
--- a/dockerfiles/scripts/chain-load.sh
+++ b/dockerfiles/scripts/chain-load.sh
@@ -40,6 +40,11 @@ elif [ "$STARTSERVER" == "SETUP" ]; then
     # Totally remove the PGDATA to force re-init on image start
     rm -Rf "${PGDATA}"
 elif [ "$STARTSERVER" == "SPAWNSET" ]; then
+    # If this is a move, then there will be no PGDATA/.spawn
+    if [ -f "${PGDATA}/.spawn" ]; then
+        exit 0;
+    fi
+
     # Execute the DB init scripts, we are already the postgres user
     # Add in MD5 auth
     echo "listen_addresses='*'" >> ${PGDATA}/postgresql.conf
@@ -52,6 +57,12 @@ elif [ "$STARTSERVER" == "SPAWNSET" ]; then
 
     echo "Creating default databases"
     eval ./prepare-databases.sh
+
+    # To stop looping init
+    echo "DONE" > "${PGDATA}/.spawn"
+    echo "Restarting server"
+    sh -c "/scripts/chain-load.sh stop"
+    sh -c "/scripts/chain-load.sh start"
 elif [ "$STARTSERVER" == "PASSRESET" ]; then
     echo "Running: password-recrypt-set"
     eval ./password-recrypt-set.sh