Docker upgrade database (#4650)

* Automate ugprading a database from 12 to 14. * parameterize source conversion and target test database service versions. --------- Co-authored-by: Damon Haley <damon.haley@nrel.gov>
SEED-platform · May 7, 2024 · 9afbe03 · 9afbe03
1 parent 1e13fae
commit 9afbe03
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diff --git a/docker-compose.build.yml b/docker-compose.build.yml
@@ -1,6 +1,6 @@
+---
 # This docker-compose version is the configuration when deploying SEED using the
 # ./deploy.sh script. This file only builds what is needed for deploying locally.
-version: "3.4"
 services:
   db-postgres:
     container_name: seed_postgres

diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -1,3 +1,4 @@
+---
 # Docker-compose setup for local development
 #
 # Configurable Values:
@@ -6,12 +7,12 @@
 #
 # Usage:
 #   docker-compose -f docker-compose.yml -f docker-compose.dev.yml up
-version: "3.4"
 services:
   db-postgres:
     container_name: seed_postgres
     volumes:
       - ref_seed_pgdata:/var/lib/postgresql/data
+      - ./share:/share
   web:
     container_name: seed_web
     image: seedplatform/seed:develop

diff --git a/docker-compose.local.yml b/docker-compose.local.yml
@@ -1,3 +1,4 @@
+---
 # Docker Compose for deployment using a local registry.
 # Must set the following environment variables
 #   POSTGRES_DB
@@ -9,7 +10,6 @@
 #   SEED_ADMIN_ORG
 #   SECRET_KEY
 
-version: "3.4"
 services:
   db-postgres:
     container_name: seed_postgres

diff --git a/docker-compose.pgupgrade.yml b/docker-compose.pgupgrade.yml
@@ -0,0 +1,62 @@
+---
+services:
+  pg13-2.14.2:
+    image: timescale/timescaledb-ha:pg13.14-ts2.14.2-oss
+    container_name: pg13-2.14.2
+    environment:
+      POSTGRES_DB: seed
+      POSTGRES_USER: seed
+      POSTGRES_PASSWORD: password
+    volumes:
+      - ./share:/share
+    restart: "no"
+  pg13-2.11.0:
+    image: timescale/timescaledb-ha:pg13.11-ts2.11.0-all
+    container_name: pg13-2.11.0
+    environment:
+      POSTGRES_DB: seed
+      POSTGRES_USER: seed
+      POSTGRES_PASSWORD: password
+    volumes:
+      - ./share:/share
+    restart: "no"
+  pg13-2.11.2:
+    image: timescale/timescaledb-ha:pg13.12-ts2.11.2-all-oss
+    container_name: pg13-2.11.2
+    environment:
+      POSTGRES_DB: seed
+      POSTGRES_USER: seed
+      POSTGRES_PASSWORD: password
+    volumes:
+      - ./share:/share
+    restart: "no"
+  pg14-2.14.2:
+    image: timescale/timescaledb-ha:pg14.11-ts2.14.2-all-oss
+    container_name: pg14-2.14.2
+    environment:
+      POSTGRES_DB: seed
+      POSTGRES_USER: seed
+      POSTGRES_PASSWORD: password
+    volumes:
+      - ./share:/share
+    restart: "no"
+  pg14-2.11.0:
+    image: timescale/timescaledb-ha:pg14.8-ts2.11.0-oss
+    container_name: pg14-2.11.0
+    environment:
+      POSTGRES_DB: seed
+      POSTGRES_USER: seed
+      POSTGRES_PASSWORD: password
+    volumes:
+      - ./share:/share
+    restart: "no"
+  pg16-2.14.2:
+    image: timescale/timescaledb-ha:pg16.2-ts2.14.2-os
+    container_name: pg16-2.14.2
+    environment:
+      POSTGRES_DB: seed
+      POSTGRES_USER: seed
+      POSTGRES_PASSWORD: password
+    volumes:
+      - ./share:/share
+    restart: "no"
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,6 +1,6 @@
+---
 # Docker Compose creates multiple containers on a single machine.
 # run `docker compose up` to create and run/link the containers
-version: "3.4"
 services:
   db-postgres:
     container_name: seed_postgres

diff --git a/docker/dump_database.sh b/docker/dump_database.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Stop the script if an error occurs
+set -e
+
+echo "Checking initial PostgreSQL and TimescaleDB versions..."
+# Show PostgreSQL version
+docker-compose exec -T db-postgres psql --user=seed -d postgres -c 'SELECT version();'
+
+# Show TimescaleDB version
+docker-compose exec -T db-postgres psql --user=seed -d postgres -c '\dx timescaledb'
+
+# Connect to the default 'postgres' database to disconnect all other users from the 'seed' database
+docker-compose exec -T db-postgres psql --user=seed -d postgres -c "SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE datname = 'seed';"
+
+docker-compose exec -T db-postgres pg_dump --username=seed --dbname=seed --verbose --no-owner --no-acl -Z7 -Fc -f "/share/seed_$(date +%Y%m%d%H%M%S).dump"
diff --git a/docker/postgres_upgrade.sh b/docker/postgres_upgrade.sh
@@ -0,0 +1,241 @@
+#!/bin/bash
+
+# Initialize variables with default values for optional parameters
+SOURCE_PG_CONV_VERSION='13'
+SOURCE_TS_CONV_VERSION='2.14.2'
+
+# Initialize variables for required parameters without default values
+TARGET_PG_TEST_VERSION=""
+TARGET_TS_TEST_VERSION=""
+
+# Parse named command line arguments
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --source-pg-conv-version)
+            SOURCE_PG_CONV_VERSION="$2"
+            shift 2
+            ;;
+        --source-ts-conv-version)
+            SOURCE_TS_CONV_VERSION="$2"
+            shift 2
+            ;;
+        --target-pg-test-version)
+            TARGET_PG_TEST_VERSION="$2"
+            shift 2
+            ;;
+        --target-ts-test-version)
+            TARGET_TS_TEST_VERSION="$2"
+            shift 2
+            ;;
+        *)
+            echo "Unknown argument: $1"
+            echo "Usage: $0 [--source-pg-conv-version <version>] [--source-ts-conv-version <version>] --target-pg-test-version <version> --target-ts-test-version <version>"
+            exit 1
+            ;;
+    esac
+done
+
+# Check if any of the required variables are still empty
+if [ -z "$TARGET_PG_TEST_VERSION" ] || [ -z "$TARGET_TS_TEST_VERSION" ]; then
+    echo "Error: Missing required arguments."
+    echo "Usage: $0 [--source-pg-conv-version <version>] [--source-ts-conv-version <version>] --target-pg-test-version <version> --target-ts-test-version <version>"
+    exit 1
+fi
+
+# Print the variables to confirm they are set
+echo "Source PostgreSQL Test Version: $SOURCE_PG_CONV_VERSION"
+echo "Source Timescale Test Version: $SOURCE_TS_CONV_VERSION"
+echo "Target PostgreSQL Test Version: $TARGET_PG_TEST_VERSION"
+echo "Target Timescale Test Version: $TARGET_TS_TEST_VERSION"
+
+# Correctly define the variables using underscores instead of hyphens
+PG_CONV_STRING="PostgreSQL ${SOURCE_PG_CONV_VERSION}"
+PG_TEST_STRING="PostgreSQL ${TARGET_PG_TEST_VERSION}"
+
+# Now print the values of these correctly named variables
+echo "PG_CONV_STRING set to: $PG_CONV_STRING"
+echo "PG_TEST_STRING set to: $PG_TEST_STRING"
+
+echo "Starting standard docker-compose dev environment..."
+docker compose -f docker-compose.yml -f docker-compose.dev.yml up -d
+
+# set intermediary source conversion postgres container from docker-compose.pgupgrade.yml
+
+# Assuming SOURCE_PG_CONV_VERSION and SOURCE_TS_CONV_VERSION have been defined earlier in the script
+echo "Setting up conversion service name from source PostgreSQL and TimescaleDB versions..."
+SOURCE_PG_TIMESCALE_CONV_SERVICE="pg${SOURCE_PG_CONV_VERSION}-${SOURCE_TS_CONV_VERSION}"
+echo "Source PostgreSQL Timescale Conversion Service set to: $SOURCE_PG_TIMESCALE_CONV_SERVICE"
+
+# Assuming TARGET_PG_TEST_VERSION and TARGET_TS_TEST_VERSION have been defined earlier in the script
+echo "Setting up test service name from target PostgreSQL and TimescaleDB versions..."
+TARGET_PG_TIMESCALE_TEST_SERVICE="pg${TARGET_PG_TEST_VERSION}-${TARGET_TS_TEST_VERSION}"
+echo "Target PostgreSQL Timescale Test Service set to: $TARGET_PG_TIMESCALE_TEST_SERVICE"
+
+# Start the specified Docker POSTGRES TIMESCALE TARGET SERVICE using docker-compose
+echo "Starting the Docker services for PostgreSQL Timescale using docker-compose..."
+docker-compose -f docker-compose.pgupgrade.yml up "${SOURCE_PG_TIMESCALE_CONV_SERVICE}" "${TARGET_PG_TIMESCALE_TEST_SERVICE}" -d
+echo "Docker services started: ${TARGET_PG_TIMESCALE_TEST_SERVICE}, ${SOURCE_PG_TIMESCALE_CONV_SERVICE}"
+
+
+echo "Starting upgrade of SEED database from Postgres 12 to $SOURCE_PG_TIMESCALE_CONV_SERVICE..."
+
+echo "Waiting for PostgreSQL to start..."
+# Wait until PostgreSQL starts and is ready to accept connections.
+until docker-compose exec -T db-postgres pg_isready -U seed -d seed > /dev/null 2>&1; do
+    echo -n "."
+    sleep 1
+done
+
+POSTGRES_VERSION=$(docker-compose exec -T db-postgres psql --user=seed -d postgres -t -A -c 'SHOW server_version;' | cut -d ' ' -f1)
+TIMESCALE_VERSION=$(docker-compose exec -T db-postgres psql --user=seed -d postgres -t -A -c "SELECT extversion FROM pg_extension WHERE extname='timescaledb';")
+
+
+echo "Disconnecting all other users from the 'seed' database..."
+docker-compose exec -T db-postgres psql --user=seed -d postgres -c "SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE datname = 'seed';"
+export PG12_DUMP="/share/seed-pg${POSTGRES_VERSION}-${TIMESCALE_VERSION}-$(date +%Y%m%d%H%M%S).dump"
+echo "Creating PostgresV: ${POSTGRES_VERSION} TimescaleV: ${TIMESCALE_VERSION} dump file of $PG12_DUMP..."
+docker-compose exec -T db-postgres pg_dump --username=seed --dbname=seed --verbose --no-owner --no-acl -Z7 -Fc -f "${PG12_DUMP}"
+
+
+echo "============================================"
+echo "Starting ${PG_CONV_STRING} Initialization Process"
+echo "============================================"
+echo "Waiting for ${SOURCE_PG_TIMESCALE_CONV_SERVICE} to start..."
+# Wait until PostgreSQL starts and is ready to accept connections.
+until docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} pg_isready -U seed -d seed > /dev/null 2>&1; do
+    echo -n "."
+    sleep 1
+done
+
+echo
+echo "${PG_CONV_STRING} is up and running."
+echo
+
+echo "Checking initial PostgreSQL and TimescaleDB versions for ${PG_CONV_STRING}..."
+# Show PostgreSQL version
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d postgres -c 'SELECT version();'
+
+# Show TimescaleDB version
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d postgres -c '\dx timescaledb'
+
+echo "Setting up database and extensions on ${PG_CONV_STRING}..."
+# Now, attempt to drop the 'seed' database
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d postgres -c 'DROP DATABASE IF EXISTS "seed";'
+
+# Create the "seed" database with the owner "seed"
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d postgres -c 'CREATE DATABASE "seed" WITH OWNER = "seed";'
+
+# Grant all privileges on the "seed" database to the user "seed"
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -c 'GRANT ALL PRIVILEGES ON DATABASE "seed" TO "seed";'
+
+# Alter the user "seed" to have CREATEDB, CREATEROLE, and SUPERUSER privileges
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -c 'ALTER USER "seed" CREATEDB CREATEROLE SUPERUSER;'
+
+# Create the PostGIS extension if it does not exist
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c 'CREATE EXTENSION IF NOT EXISTS postgis;'
+
+echo "Dropping TimescaleDB extension to prepare for reinstallation or update..."
+# Drop the TimescaleDB extension
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c "DROP EXTENSION timescaledb;"
+
+echo "Pausing to ensure all database operations have ceased before proceeding..."
+# Wait a moment (optional, might be needed in very fast consecutive executions)
+sleep 10
+
+echo "Creating the TimescaleDB extension with the specified version..."
+# Create the extension
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c "CREATE EXTENSION IF NOT EXISTS timescaledb WITH VERSION '${TARGET_TS_TEST_VERSION}' ;"
+
+echo "Verifying the TimescaleDB extension is installed correctly..."
+# Check the extension
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c '\dx timescaledb'
+
+echo "Preparing the database for restore operations..."
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c 'SELECT timescaledb_pre_restore();'
+
+# Restore from backup
+echo "Restoring postgres 12 database ${PG12_DUMP} from backup..."
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} pg_restore --exit-on-error --no-owner --no-acl --user=seed -d seed -v ${PG12_DUMP}
+
+echo "Performing post-restore operations for TimescaleDB..."
+# Post restore with TimescaleDB
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c 'SELECT timescaledb_post_restore();'
+
+echo "Verifying the TimescaleDB extension post-restore..."
+# Check the extension again
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c '\dx timescaledb'
+
+echo "Updating TimescaleDB extension to ensure it's at the latest compatible version..."
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d seed -c 'ALTER EXTENSION timescaledb UPDATE;'
+
+# Capture the PostgreSQL version from the container
+POSTGRES_VERSION=$(docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d postgres -t -A -c 'SHOW server_version;' | cut -d ' ' -f1)
+
+# Capture the TimescaleDB version from the container using SQL command
+TIMESCALE_VERSION=$(docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} psql --user=seed -d postgres -t -A -c "SELECT extversion FROM pg_extension WHERE extname='timescaledb';")
+export CONV_DUMP="/share/seed-pg${POSTGRES_VERSION}-${TIMESCALE_VERSION}-$(date +%Y%m%d%H%M%S).dump"
+echo "Dumping upgraded Postgres Version: ${POSTGRES_VERSION}, TimescaleDB Version: ${TIMESCALE_VERSION} to file: ${CONV_DUMP}..."
+docker-compose exec -T ${SOURCE_PG_TIMESCALE_CONV_SERVICE} pg_dump --username=seed --dbname=seed --verbose --no-owner --no-acl -Z7 -Fc -f "${CONV_DUMP}"
+
+
+echo "============================================"
+echo "Transitioning to ${PG_TEST_STRING}"
+echo "============================================"
+
+echo "Waiting for ${TARGET_PG_TIMESCALE_TEST_SERVICE} to start..."
+# Wait until ${PG_TEST-STRING} starts and is ready to accept connections.
+until docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} pg_isready -U seed -d seed > /dev/null 2>&1; do
+    echo -n "."
+    sleep 1
+done
+
+echo
+echo "${PG_TEST_STRING} is up and running."
+echo
+
+echo "Checking initial PostgreSQL and TimescaleDB versions for ${PG_TEST-STRING}..."
+# Show PostgreSQL version
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d postgres -c 'SELECT version();'
+
+# Show TimescaleDB version
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d postgres -c '\dx timescaledb'
+
+echo "Setting up database and extensions on ${PG_TEST-STRING}..."
+
+# Now, attempt to drop the 'seed' database
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d postgres -c 'DROP DATABASE IF EXISTS "seed";'
+
+# Create the "seed" database with the owner "seed"
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d postgres -c 'CREATE DATABASE "seed" WITH OWNER = "seed";'
+
+# Grant all privileges on the "seed" database to the user "seed"
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -c 'GRANT ALL PRIVILEGES ON DATABASE "seed" TO "seed";'
+
+# Alter the user "seed" to have CREATEDB, CREATEROLE, and SUPERUSER privileges
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -c 'ALTER USER "seed" CREATEDB CREATEROLE SUPERUSER;'
+
+# Create the PostGIS extension if it does not exist
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d seed -c 'CREATE EXTENSION IF NOT EXISTS postgis;'
+
+# Prepare for restore with TimescaleDB
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d seed -c 'SELECT timescaledb_pre_restore();'
+
+echo "Restoring ${PG_CONV_STRING} database ${CONV_DUMP} from backup..."
+# Restore from backup
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} pg_restore --exit-on-error --no-owner --no-acl --user=seed -d seed -v ${CONV_DUMP}
+
+# Prepare for restore with TimescaleDB
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d seed -c 'SELECT timescaledb_post_restore();'
+
+# Capture the PostgreSQL version from the containerP
+POSTGRES_VERSION=$(docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d postgres -t -A -c 'SHOW server_version;' | cut -d ' ' -f1)
+TIMESCALE_VERSION=$(docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} psql --user=seed -d postgres -t -A -c "SELECT extversion FROM pg_extension WHERE extname='timescaledb';")
+export TEST_DUMP="/share/seed-pg${POSTGRES_VERSION}-${TIMESCALE_VERSION}-$(date +%Y%m%d%H%M%S).dump"
+echo "Dumping upgraded PostgresV: ${POSTGRES_VERSION} TimescaleV: ${TIMESCALE_VERSION} file of $TEST_DUMP..."
+docker-compose exec -T ${TARGET_PG_TIMESCALE_TEST_SERVICE} pg_dump --username=seed --dbname=seed --verbose --no-owner --no-acl -Z7 -Fc -f "${TEST_DUMP}"
+
+export COMPOSE_FILE=docker-compose.pgupgrade.yml
+docker-compose stop ${SOURCE_PG_TIMESCALE_CONV_SERVICE}
+docker-compose stop ${TARGET_PG_TIMESCALE_TEST_SERVICE}
+unset COMPOSE_FILE
+echo "Database operations completed."