MG-4: Add OpenELIS db setup script and update PostgreSQL init process (#226)

Author: kipchubett

distro/data/postgresql/create_db.sh

@@ -5,13 +5,19 @@
 # Workaround for PostgreSQL Docker image not running files from sub-dirs.
 # https://github.com/docker-library/postgres/issues/605#issuecomment-567236795
 #
+# Only execute shell scripts (*.sh) found in the subdirectories so that
+# SQL files are not interpreted by the shell (they should be applied via
+# psql from the shell scripts that know how to apply them).
 #
 set -e
 directory=/docker-entrypoint-initdb.d/db/
 if [ -d "${directory}" ]
 then
-    find ${directory}* -type f -execdir ls {} \; -execdir bash {} \;
+    # Find and execute only shell scripts. execdir runs the command from the
+    # directory where the matched file is located, which preserves relative
+    # paths used by the scripts.
+    find "${directory}" -type f -name '*.sh' -execdir ls {} \; -execdir bash {} \;
 else
     echo "Directory '${directory}' does not exist. No database to create. Exit 0."
 fi
-exit 0
+exit 0

distro/data/postgresql/openelis/create_db_and_user.sh

@@ -0,0 +1,80 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+echo "Setting up OpenELIS database, users and loading schema..."
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+echo "Using script dir: ${SCRIPT_DIR}"
+
+export db_name=$OPENELIS_DB_NAME
+export db_schema=$OPENELIS_DB_SCHEMA
+export db_username=$OPENELIS_DB_USER
+export db_password=$OPENELIS_DB_PASSWORD
+export db_admin_password=$OPENELIS_DB_ADMIN_PASSWORD
+
+createuser "${db_username}"
+createdb "${db_name}"
+
+psql -d "${db_name}" -c "alter user ${db_username} with password '${db_password}';"
+psql -d "${db_name}" -c "grant all privileges on database ${db_name} to ${db_username};"
+psql -d "${db_name}" -c "create schema ${db_schema};"
+psql -d "${db_name}" -c "alter schema ${db_schema} owner to ${db_username};"
+
+# Assign ownership of the database to the created user
+psql -d "${db_name}" -c "ALTER DATABASE ${db_name} OWNER TO ${db_username};"
+echo "Database '${db_name}' ownership assigned to user '${db_username}'."
+
+echo "Database '${db_name}' and user '${db_username}' created."
+
+# create a superuser for the database
+psql -d "${db_name}" -c "create user admin with superuser;"
+psql -d "${db_name}" -c "alter user admin with password '${db_admin_password}';"
+echo "Superuser 'admin' created."
+
+# Path to SQL files
+OPENELIS_SQL="${SCRIPT_DIR}/OpenELIS-Global.sql"
+SITEINFO_SQL="${SCRIPT_DIR}/siteInfo.sql"
+
+# Ensure files exist
+if [[ ! -f "${OPENELIS_SQL}" ]]; then
+  echo "ERROR: ${OPENELIS_SQL} not found" >&2
+  exit 1
+fi
+if [[ ! -f "${SITEINFO_SQL}" ]]; then
+  echo "ERROR: ${SITEINFO_SQL} not found" >&2
+  exit 1
+fi
+
+if [[ -f "${OPENELIS_SQL}" ]]; then
+  awk '{
+    orig=$0
+    lo=tolower($0)
+    if (lo ~ /^[[:space:]]*create[[:space:]]+schema[[:space:]]+clinlims[[:space:]]*;[[:space:]]*$/ && lo !~ /if[[:space:]]+not[[:space:]]+exists/) {
+      if (orig !~ /^[[:space:]]*--/) {
+        print "-- " orig
+        next
+      }
+    }
+    print
+  }' "${OPENELIS_SQL}" > "${OPENELIS_SQL}.tmp"
+
+  if ! cmp -s "${OPENELIS_SQL}" "${OPENELIS_SQL}.tmp"; then
+    echo "Backing up ${OPENELIS_SQL} to ${OPENELIS_SQL}.bak"
+    cp "${OPENELIS_SQL}" "${OPENELIS_SQL}.bak"
+    mv "${OPENELIS_SQL}.tmp" "${OPENELIS_SQL}"
+    echo "Commented out plain CREATE SCHEMA clinlims; in ${OPENELIS_SQL}"
+  else
+    rm "${OPENELIS_SQL}.tmp"
+    echo "No plain 'CREATE SCHEMA clinlims;' found or already commented/has IF NOT EXISTS; no change."
+  fi
+fi
+
+# Load schema/data into the newly created database
+echo "Loading ${OPENELIS_SQL} into ${db_name}..."
+psql -v ON_ERROR_STOP=1 --username admin --dbname "$db_name" -f "${OPENELIS_SQL}"
+
+echo "Loading ${SITEINFO_SQL} into ${db_name}..."
+psql -v ON_ERROR_STOP=1 --username admin --dbname "$db_name" -f "${SITEINFO_SQL}"
+
+echo "SQL files imported successfully."