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iRODS hands-on for admins

This tutorial explains how to administrate users and resources as irods admin. We will work with the icommands installed on the user interface machine. You will need irodsadmin rights and sudo rights on the iRODS server (e.g. alice-server).

The iadmin mode

Creating users and resources are done under the iadmin mode. You can enter this mode by typing

iadmin #start mode
help
q #quit mode

In this mode you can only execute iadmin commands listed under help but not the 'normal' icommands such as iput. Alternatively, all iadmin commands can be executed directly on the shell predeeded with 'iadmin'.

iadmin help

User admnistration with iadmin

Exercise Inspect the function iadmin mkuser and iadmin moduser and create a "rodsuser" and a "rodsadmin".
iadmin mkuser create a user
iadmin moduser modify user attributes
iadmin rmuser delete a user
iadmin mkgroup create group

iRODS resources

In iRODS you can create so-called resources which correspond to different physical locations such as resource servers and storage devices. There are two types of of resources, coordinating and storage resources. By combining them you can create large decision trees with storage resources as leaves and coordinating resources to decide where the data should go to.

Recall that with ilsresc you can list all existing resources in your iRODS zone. Let's create a new resource in your home directory on alice-server (the server on which iRODS is installed). To this end we create a new directory called newVault and declare it as a new storage resource.

iadmin mkresc newResc unixfilesystem <fully qualified hostname>:/home/alice/newVault

Since iRODS is executed not as your local user but as irods, putting data into the resource located in your home directpry will fail:

iput -R newResc put2.txt
ERROR: putUtil: put error for /alicetestZone/home/alice/put2.txt,
 status = -520013 status = -520013 UNIX_FILE_MKDIR_ERR, Permission denied

This can be helped by granting read and write access to the irods user. Usually resources are created directly under /var/lib/irods.

Composable resource trees

We will now create a resource tree in which data will be replicated automatically between two resources. When you are working on our training machines please create the resources in your home directory and set the read and write access for the irods user. If you are working on your own machine you can create the resources directly under /var/lib/irods or somewhere higher up the directory tree.

1. Create a the physical resource First we will create the physical locations for the resources on the iRODS server:

sudo mkdir /var/lib/irods/iRODS/storage1
sudo mkdir /var/lib/irods/iRODS/storage2

2. Create two unix file system resources Now we can include these two resources as storage resources in iRODS:

iadmin mkresc storage1 unixfilesystem <fully qualified hostname>:/var/lib/irods/iRODS/storage1
iadmin mkresc storage2 unixfilesystem <fully qualified hostname>:/var/lib/irods/iRODS/storage2

All iRODS users will have access to these two resources.

3. Create a coordinating replication resource

iadmin mkresc replResc replication

The keyword replication triggers the behaviour of this cordinating resource. All data in this resource will be automatically replicated between the two storage resources.

4. Connect the resources

iadmin addchildtoresc replResc storage1
iadmin addchildtoresc replResc storage2

We can inspect the resource tree and put data. Usually data is put into the coordinating resource, i.e. replResc. From there the data replicated to the two leaves, storage1 and storage2.

ilsresc
iput -R replResc test.txt
ils -L put2.txt
  alice             0 replResc;storage2           13 2016-05-05.00:12 & put2.txt
        generic    /var/lib/irods/iRODS/storage2/home/alice/put2.txt
  alice             1 replResc;storage1           13 2016-05-05.00:12 & put2.txt
        generic    /var/lib/irods/iRODS/storage1/home/alice/put2.txt

Resource trees implement data policies on the system level. You can find a full list of preimplemented coordinating storage resources here
iadmin mkresource create a resource
iadmin rmresc delete a resource
iadmn modresc modify resource attributes

Exercises

  1. Try to send data directly to storage2 or storage1.
  2. Modify the replication resource to the type roundrobin and test where newly ingested data will be saved. Hint: upload several files.

Compound resources

Compound resources consist of a cache resource and an archive resource. Data is entered to the cache resource and passed later to the archive resource. The archive resource can be of several storage types for which one might need to adapt the data transfer protocol. This is defined in /var/lib/irods/iRODS/server/bin/cmd/univMSSInterface.sh

To create such a compound resource, please refer to this setup.

Exercise Inspect the univMSSInterface.sh and adopt it to work with rsync or another transfer protocol.
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