iRODS

The Integrated Rule-Oriented Data System (iRODS) is a tool that provides transparent access to data distributed on different sites and on heterogeneous backends (disk filesystems, databases, tape systems etc.)

Get an account

You need an iRODS account to be able to use it at CC-IN2P3, which you can ask by contacting the user support. Once your request is approved, you will receive your connection parameters.

Use the iCommands

The iCommands are the Unix and Windows command-line utilities that interface to the iRODS system.

From an interactive server

If you have an account at CC-IN2P3, you may connect to the interactive machines and use the iCommands:

% ssh cca.in2p3.fr
% module load irods
% which iinit
/pbs/software/centos-7-x86_64/irods/3.3.1/bin/iinit

The iCommands version corresponding to your profile will be automatically selected.

In the vast majority of use cases, you will not need to choose a particular version of the iCommands. Nonetheless, if you wish to use a particular version of the iCommands, you can use the following command to display the available versions:

% module view irods
/pbs/software/centos-7-x86_64/modules/modulefiles

DataManagement/irods :
  - 3.3.1
  - 4.1.8
  - 4.2.1
  - 4.2.10
  - 4.2.11
  - 4.2.2
  - 4.2.3
  - 4.2.6
  - 4.2.9
  - default  (alias: irods)

And then:

% module load DataManagement/irods/<version>

For example, if you want to use version 4.2.10:

% module load DataManagement/irods/4.2.10
% which iinit
/pbs/software/centos-7-x86_64/irods/4.2.10/bin/iinit

From an external machine

Please refer to the paragraph Get the iRODS client to download and install the useful binaries.

Create the connection parameters

Create a directory ${HOME}/.irods and create a file ${HOME}/.irods/.irodsEnv that contains the necessary information:

irodsHost <irods-hostname>
irodsPort <irods-port-number>
irodsHome <irods-home-dir>
irodsCwd <irods-home-dir>
irodsUserName <irods-username>
irodsZone <irods-zone-name>

Get started with iCommands

First of all, execute the iinit command, which asks for the password of your iRODS account defined in the file .irodsEnv. iinit encrypts the password and stores it into a file named .irodsA.

Once done, you should not need to provide your password again for further iCommands. To clean the encrypted password please run the command iexit.

Warning

File names must NOT contain any accents or special characters like #?! * etc.

Please find below the list of the mostly used iCommands. Use the -h option with the command of your choice to learn more.

iCommand Description
icd Changes the working directory
ichmod Gives access/grants permissions to another user
iexit Logs off/disconnects from iRODS
iget Downloads the file/directory from iRODS to local device
init Initializes and starts the connection to iRODS
ils Lists the contents of the current working directory
imeta Manages user-defined metadata
imkdir Creates a new directory
iput Uploads the file/directory from the local device to iRODS
ipwd Shows the name and path of the current remote folder
irm Moves a file to the trash
irsync Synchronize a folder from a local directory to a directory in iRODs

You can find more information about the iCommands on the iRODS documentation Web page.

Manage metadata

Metadata are data about your data. In iRODS metadata include system and user-defined attributes associated with a Data-Object, Collection, Resource etc. stored in the iCAT database.

To add, remove, list or query user-defined metadata, use the command imeta:

% imeta
Usage: imeta [-vVh] [command] Commands are:

add -d|C|R|u Name AttName AttValue [AttUnits] (Add new AVU triplet)
rm  -d|C|R|u Name AttName AttValue [AttUnits] (Remove AVU)
rmw -d|C|R|u Name AttName AttValue [AttUnits] (Remove AVU, use Wildcards)
ls  -d|C|R|u Name [AttName] (List existing AVUs for item Name)
lsw -d|C|R|u Name [AttName] (List existing AVUs, use Wildcards)
qu -d|C|R|u AttName Op AttVal  (Query objects with matching AVUs)
cp -d|C|R|u -d|C|R|u Name1 Name2 (Copy AVUs from item Name1 to Name2)

With imeta you can add metadata to: Data-Object, Collection, User.

A metadata is defined as a triplet containing the:

  • Attribute Name (AttName)
  • Attribute Value (AttVal)
  • Attribute Unit (AttUnits)

Add metadata to a collection /tempZone/home/calvat/images:

% imeta add -C /tempZone/home/calvat/images type tiff
% imeta add -C /tempZone/home/calvat/images zone isere

List metadata:

% imeta ls -C /tempZone/home/calvat/images
AVUs defined for collection /tempZone/home/calvat/images:
attribute: type
value: tiff
unit:
----
attribute: zone
value: isere
unit:

Remove metadata:

% imeta rm -C /tempZone/home/calvat/images/montagne type tiff

Search data with metadata:

% imeta qu -C zone = isere
collection: /tempZone/home/calvat/images

Migration to Tape system

Upon request, we can trigger the migration of your incoming iRODS data to our hierarchical tape system HPSS. Please contact the user support to activate this mechanism.

Get the iRODS client

To connect to an iRODS server from your machine, you may download the version 4.x client from the project web site or use the package manager of your machine.

To download the version 3.x clients, select the archive corresponding to your operating system from the list below. Next, unzip the archive and adjust your environment variable PATH accordingly.

Keep in mind that to connect to 3.3.1 servers a 3.3.1 client is needed in the same way that for a 4.x server a 4.x client is needed.

Note

As of version 3.0, it may be necessary to install the Microsoft Visual Studio libraries.

It is also possible to use iRODS through Java APIs using the jargon package.

For Windows, there is a graphical client which allows to navigate in the iRODS tree in a user-friendly way.