ioos/i52n-sos repository overview

⁠IOOS 52°North SOS

This repository holds the IOOS custom modules for the 52°North Sensor Observation System⁠.

See the project page at http://ioos.github.io/i52n-sos⁠ for user documentation.

⁠Docker

These examples require Docker 1.9.0 or higher. Older versions will work with adjustments left to the user (don't use named volume).

Please review the Docker documentation⁠ if you aren't familiar with Docker.

⁠Run i52n-sos on port 8083 using a pre-built image on the IOOS Docker Hub repository

docker run -d -p 8083:8080 -v i52n-sos:/srv/i52n-sos \
  --name i52n-sos --restart=unless-stopped ioos/i52n-sos:1.1

This will store configuration data in the i52n-sos named volume which will survive removal of and recreation of the i52n-sos container.

The i52n-sos main page will be available at http://localhost:8083⁠

The i52n-sos service endpoint will be available at http://localhost:8083/service⁠

⁠View logs

docker logs i52n-sos

⁠Stop the running container

docker stop i52n-sos

⁠Remove the container (if you need to adjust port, etc)

docker rm i52n-sos

⁠Start the stopped container

docker start i52n-sos

⁠Delete the configuration volume

docker volume rm i52n-sos

⁠Increase Tomcat memory

First, create a setenv.sh file to set the JAVA_OPTS used by Tomcat. Example:

JAVA_OPTS="-Djava.awt.headless=true -Xmx4G -XX:+UseConcMarkSweepGC"

Then, provide this file to Tomcat inside the i52n-sos container when running in Docker. Example:

docker run -d -p 8083:8080 -v i52n-sos:/srv/i52n-sos \
  -v $(pwd)/setenv.sh:/usr/local/tomcat/bin/setenv.sh
  --name i52n-sos --restart=unless-stopped ioos/i52n-sos:1.1

⁠Run a PostgreSQL/PostGIS server and i52n-sos together in Docker

Copy the example database init script⁠ to your server, rename it to init-db.sh, and edit the sos user's password. Then:

docker network create i52n-sos 2>/dev/null

docker run -d --restart=always --net i52n-sos -e POSTGRES_PASSWORD=SOME_PASSWORD -p 5435:5432 \
  -v $(pwd)/init-db.sh:/docker-entrypoint-initdb.d/init-db.sh \
  -v i52n-sos-db:/var/lib/postgresql/data \
  --name i52n-sos-db mdillon/postgis:9.5

docker run -d --restart=always --net i52n-sos -p 8083:8080 -v i52n-sos:/srv/apps/i52n-sos \
  --name i52n-sos --restart=always ioos/i52n-sos:1.1

i52n-sos-db's database will be exposed on the host on port 5435, but it is available to the i52n-sos container within the i52n-sos Docker network on 5432 (the normal PostgreSQL port).

When setting up the SOS datasource in the installer, use i52n-sos-db as the database host, 5432 as the port, sos as the username, and the password you set for the sos user in init-db.sh.

To see logs for the PostgreSQL/PostGIS server:

docker logs i52n-sos-db

Note that this will run PostgreSQL with the default configuration. You will likely need to adjust memory settings by issuing ALTER SYSTEM commands, e.g.

ALTER SYSTEM SET shared_buffers = '4096MB';
ALTER SYSTEM SET max_connections = 200;
ALTER SYSTEM SET work_mem = '160MB';
ALTER SYSTEM SET effective_cache_size = '11GB';
ALTER SYSTEM SET maintenance_work_mem = '960MB';

And then restarting the container:

docker restart i52n-sos-db

Alternatively you can customize a postgres.conf file and pass it to the container using a volume at /var/lib/postgresql/data/postgres.conf.

⁠Backup i52n configuration

docker run --rm -v i52n-sos:/srv/apps/i52n-sos -v $(pwd):/backup debian:jessie \
  tar cvf /backup/i52n-sos-backup.tar /srv/apps/i52n-sos

This will backup the i52n-sos configuration to i52n-sos-backup.tar. Note that the tarball will be owned by root.

⁠Restore i52n configuration

docker stop i52n-sos 2> /dev/null

docker run --rm -v i52n-sos:/srv/apps/i52n-sos -v $(pwd)/i52n-sos-backup.tar:/tmp/backup.tar \
  debian:jessie bash -c "rm -rf /src/app/i52n-sos/* && tar xvf /tmp/backup.tar --strip 1"

docker start i52n-sos

⁠Backup and restore PostgreSQL/PostGIS database

Data in the PostgreSQL/PostGIS database should back backed up and restored normally, e.g using pg_dump and pg_restore.

Note that you will be prompted for the POSTGRES_PASSWORD you set when you created the i52n-sos-db container. You can set up a .pgpass⁠ file to avoid this. If you forgot the Postgres password, try

docker exec -it i52n-sos-db bash -c "echo \$POSTGRES_PASSWORD"

pg_dump --host localhost --port 5435 --user postgres -Fc sos --file i52n-sos-db.pgbackup

pg_restore --host localhost --port 5435 --user postgres --dbname sos --clean i52n-sos-db.pgbackup

If you don't have psql installed or can't connect to i52n-sos-db because of version issues, you can run the same commands inside a Docker container:

docker run -it --rm --net i52n-sos -v $(pwd):/backup mdillon/postgis:9.5 \
  pg_dump --host i52n-sos-db --port 5432 --user postgres -Fc \
  sos --file /backup/i52n-sos-db.pgbackup

docker run -it --rm --net i52n-sos -v $(pwd)/i52n-sos-db.pgbackup:/tmp/backup.pgbackup \
  mdillon/postgis:9.5 pg_restore --host i52n-sos-db --port 5432 \
  --user postgres --dbname sos --clean /tmp/backup.pgbackup