Experimental new docker system that will work with volume_mounts

dockerfiles/ehrbase-postgresql-full.dockerfile

@@ -3,56 +3,65 @@ 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"
 
 # 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 init scripts to init directory
-COPY ./scripts/create-ehrbase-user.sh /docker-entrypoint-initdb.d/
+# Copy system scripts to the scripts directory on root
+COPY scripts /scripts
+RUN chmod +x /scripts/*
+
+# Install python and dependencies
+RUN apk add --update postgresql=${PG_MAJOR}-r0 \
+    build-base  \
+    git         \
+    flex        \
+    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"
 
-# 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
+RUN echo "DONE" > /scripts/.pginit
 
-# 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
+# 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 echo "Enforcing ownership, one moment" \
+    && chown -R postgres:postgres ${PGDATA}
 
 EXPOSE 5432

dockerfiles/scripts/chain-load.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+# Read in ARG0
+STARTSERVER="$1";
+
+# Always swap to /scripts
+cd /scripts
+
+# Always expand the enviroment
+set -e
+
+# Incase this is a volume mount move
+if [ -f "/scripts/.pginit" ]; then
+    STARTSERVER="SPAWNSET"
+fi
+
+if [[ -z "$STARTSERVER" ]]; then
+    echo "No runmode specified!"
+    exit 0
+else
+    echo "Running mode: $STARTSERVER"
+fi
+
+# 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
+    # 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='*'" >> ${PGDATA}/postgresql.conf
+
+    echo "Running temporal table test"
+    eval ./test-temporal-tables.sh
+
+    echo "Running: create-ehrbase-user"
+    eval ./create-ehrbase-user.sh
+
+    echo "Creating default databases"
+    eval ./prepare-databases.sh
+
+    # To stop looping init
+    echo "DONE" > "${PGDATA}/.spawn"
+    echo "Restarting server"
+    sh -c "/scripts/chain-load.sh stop"
+    sh -c "/scripts/chain-load.sh start"
+elif [ "$STARTSERVER" == "PASSRESET" ]; then
+    echo "Running: password-recrypt-set"
+    eval ./password-recrypt-set.sh
+else
+    echo "Unknown action '$STARTSERVER' called."
+fi;

dockerfiles/scripts/create-ehrbase-user.sh

@@ -1,12 +1,10 @@
 #!/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 ${EHRBASE_USER};
-    CREATE USER root WITH SUPERUSER;
-EOSQL
+echo "Creating user(${EHRBASE_USER}) pass(${EHRBASE_PASSWORD}) db(ehrbase)"
 
-# Stop database before proceeding
-su - postgres -c "pg_ctl -D ${PGDATA} -w stop"
+psql -U "${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

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

dockerfiles/scripts/prepare-databases.sh

@@ -1,21 +1,15 @@
 #!/bin/bash
 
-set -e
-
-# Start server
-su - postgres -c "pg_ctl -D ${PGDATA} -w start"
+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 $EHRBASE_USER;
+CREATE SCHEMA IF NOT EXISTS ehr AUTHORIZATION "$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"

dockerfiles/scripts/test-temporal-tables.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd /scripts/temporal_tables
+
+# Build from source
+make installcheck