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