mjstealey/docker-irods-icat

Docker implementation of iRODS ICAT server using PostgreSQL

docker-irods-icat

Docker implementation of iRODS iCAT Server using PostgreSQL 9.4

Supported tags and respective Dockerfile links

• 4.1.10, latest (4.1.10/Dockerfile)
• 4.1.9 (4.1.9/Dockerfile)
• 4.1.8 (4.1.8/Dockerfile)
• 4.1.7 (4.1.7/Dockerfile)

4.2.x (4.2.0-preview) This pre-release is for TESTING ONLY - do not use this on production deployments.

Docker image

Pull image from dockerhub

docker pull mjstealey/docker-irods-icat:latest

Usage:

Example 1. Deploy with default configuration

docker run --name icat mjstealey/docker-irods-icat:latest

This call can also be daemonized with the -d flag, which would most likely be used in an actual environment.

On completion a running container named icat is spawned with the following configuration:

-------------------------------------------
iRODS Zone:                 tempZone
iRODS Port:                 1247
Range (Begin):              20000
Range (End):                20199
Vault Directory:            /var/lib/irods/iRODS/Vault
zone_key:                   TEMPORARY_zone_key
negotiation_key:            TEMPORARY_32byte_negotiation_key
Control Plane Port:         1248
Control Plane Key:          TEMPORARY__32byte_ctrl_plane_key
Schema Validation Base URI: https://schemas.irods.org/configuration
Administrator Username:     rods
Administrator Password:     Not Shown (rods)
-------------------------------------------
-------------------------------------------
Database Type:     postgres
Hostname or IP:    localhost
Database Port:     5432
Database Name:     ICAT
Database User:     irods
Database Password: Not Shown (irods)
-------------------------------------------

Use the docker exec call to at the terminal interact with the container. Add the user definition of -u irods to specify that commands should be run as the irods user which is the systme user assigned to rodsadmin.

• Sample ils:

  $ docker exec -u irods icat ils
  /tempZone/home/rods:
  

• Sample iadmin lz

  $ docker exec -u irods icat iadmin lz
  tempZone
  

Example 2. Use an environment file to pass the required environment variables for the iRODS setup_irods.sh call.

$ docker run --env-file sample-env-file.env --name icat mjstealey/docker-irods-icat:latest

• Using sample environment file named sample-env-file.env (Update as required for your iRODS installation)

  IRODS_SERVICE_ACCOUNT_NAME=irods
  IRODS_SERVICE_ACCOUNT_GROUP=irods
  IRODS_ZONE_NAME=tempZone
  IRODS_PORT=1247
  IRODS_PORT_RANGE_BEGIN=20000
  IRODS_PORT_RANGE_END=20199
  IRODS_VAULT_DIRECTORY=/var/lib/irods/iRODS/Vault
  IRODS_SERVER_ZONE_KEY=TEMPORARY_zone_key
  IRODS_SERVER_NEGOTIATION_KEY=TEMPORARY_32byte_negotiation_key
  IRODS_CONTROL_PLANE_PORT=1248
  IRODS_CONTROL_PLANE_KEY=TEMPORARY__32byte_ctrl_plane_key
  IRODS_SCHEMA_VALIDATION=https://schemas.irods.org/configuration
  IRODS_SERVER_ADMINISTRATOR_USER_NAME=rods
  IRODS_SERVER_ADMINISTRATOR_PASSWORD=rods
  IRODS_DATABASE_SERVER_HOSTNAME=localhost
  IRODS_DATABASE_SERVER_PORT=5432
  IRODS_DATABASE_NAME=ICAT
  IRODS_DATABASE_USER_NAME=irods
  IRODS_DATABASE_PASSWORD=irods

This call can also be daemonized with the -d flag, which would most likely be used in an actual environment.

On completion a running container named icat is spawned with the same configuration as in the first example.

• Sample iadmin lr:

  $ docker exec -u irods icat iadmin lr
  bundleResc
  demoResc
  

• Sample iadmin lu

  $ docker exec -u irods icat iadmin lu
  rods#tempZone
  

Example 3. Sharing host volume with container for persisting database or Vault

The container exposes two volume mount points for PostgreSQL data and iRODS Vault data.

• PostgreSQL data: /var/lib/postgresql/data
• iRODS Vault data: /var/lib/irods/iRODS/Vault

The host can mount local volumes corresponding to these in order to preserve the iRODS installation between runs of the docker container. Say we want to map /LOCAL_POSTGRES to /var/lib/postgresql/data and /LOCAL_IRODS to /var/lib/irods/iRODS/Vault, we would run something like this.

$ docker run \
  -v /LOCAL_POSTGRES:/var/lib/postgresql/data \
  -v /LOCAL_IRODS:/var/lib/irods/iRODS/Vault \
  --name icat \
  mjstealey/docker-irods-icat:latest

Using a local directory named /mydata for postgres data and another local directory /myvault for the iRODS vault with our setup configuration in the sample-env.env file we would run this.

$ docker run \
  -v /mydata:/var/lib/postgresql/data \
  -v /myvault:/var/lib/irods/iRODS/Vault \
  --env-file sample-env-file.env \
  --name icat \
  mjstealey/docker-irods-icat:latest

On completion a running container named icat is spawned with the configuration as defined in the sample-env.env file and if we were to look in the local /mydata and myvault directories we would see the following.

PostgreSQL /mydata

$ sudo ls /mydata/ -1
base
global
pg_clog
pg_dynshmem
pg_hba.conf
pg_ident.conf
pg_logical
pg_multixact
pg_notify
pg_replslot
pg_serial
pg_snapshots
pg_stat
pg_stat_tmp
pg_subtrans
pg_tblspc
pg_twophase
PG_VERSION
pg_xlog
postgresql.auto.conf
postgresql.conf
postmaster.opts
postmaster.pid

NOTE - sudo is required because the files are owned by the postgres user within the container which may not have a corresponding user on the local file system. The postgres user has UID=999, GID=999.

iRODS Vault /myvault

$ sudo ls /myvault/
home
$ sudo ls /myvault/home
rods

NOTE - sudo is required because the files are owned by the irods user within the container which may not have a corresponding user on the local file system. The irods user has UID=998, GID=998.

TODO: attach to persisted data on subsequent runs of container or destruction of container