Archiving with iRODS

iRODS stands for integrated Rule-Oriented Data System iRODS and is an Open Source Data Management software. It is a kind of a virtual file system, with its own lingo:

• folders are called collections, they may contain further subcollections
• files are (data objects).

All commands from the iRODS command line tools start with an 'i' and they are installed on the mogon login nodes.

iRODS uses so called 'Resources' to archive the collections and data objects. The resources are organized hierarchically. The root is a replication resource, where other resources are added as children. Currently there is a compound resource consisting itself of a cache (unix filesystem) and a universal mass storage system (here: TSM) as archive. The cache has a size of 8TB, once it is fills up, the oldest data objects will be deleted on the cache. If required, they will be fetched back from the archive.

replResc:replication
├── cephfsResc:unixfilesystem
└── compResc:compound
    ├── netappResc:unixfilesystem
    └── tsmResc:univmss

On request it is still possible to apply for a TSM account, to store the data on tapes.

• (Raw) input data
• Final publishable or already published data
• zipped (git) repositories of the scripts/software used to process the data.

Intermediate results and work in progress do not belong in an archive.

If a directory, resp. collection, consists of many small files, those files should be compressed. iRODS works best for files > 5GB.

There is no need to apply for an iRODS archiving account. Every user of MOGON I/II automatically gets access to iRODS. If your account is associated with a MOGON project you also get read/write access to the iRODS project collection ( /zdv/project/<PROJECT NAME> )

Each user has a hidden directory ${HOME}/.irods with the file irods_environment.json in the mogon home directory containing the connection information for the iRODS archive. Below you see the information template for irods_environment.json.

{
    "irods_client_server_negotiation": "request_server_negotiation",
    "irods_client_server_policy": "CS_NEG_REQUIRE",
    "irods_authentication_scheme": "KRB",
    "irods_host": "irods.zdv.uni-mainz.de",
    "irods_port": 1247,
    "irods_user_name": "<$USER>",
    "irods_zone_name": "zdv",
    "irods_encryption_key_size": 32,
    "irods_encryption_salt_size": 8,
    "irods_encryption_num_hash_rounds": 16,
    "irods_encryption_algorithm": "AES-256-CBC"
}

Authentication is done via kerberos. To get access to the iRODS archive, use the kinit command and enter your password. Please do not use iinit, it will not work and change your `${HOME}/.irods/irods_environment.json` file. In case it happened, remove the folder `${HOME}/.irods` and login again, it will be restored on login.

Here is a short summary over the most important iRODS commands with some important command line parameters.

As mentioned above, iRODS is a kind of a virtual filesystem. The following commands can be used to for navigation.

Each user gets his/her personal home under /zdv/home/${USER} and access to the associated Mogon I/II projects under /zdv/project/<PROJECT NAME>.

Accessible folders:

• /zdv/home/${USER} private directory
• /zdv/project/<PROJECT NAME> project directory
• /zdv/home/public every registered user can read/write/delete
• /zdv/trash/home/${USER} private trash bin

Uploading data to the iRODS-Archive is done with the command iput.

The checksum is calculated server side and we highly recommend to switch it on immediately on upload. Nevertheless, You can also do it later on with ichksum -K <filename>. It creates a checksum equivalent to the command sha256sum <local filename> | cut -d “ ” -f 1 | xxd -r -p | base64, which you can compare to ensure data integrity. The checksums can be queried with ils -L and ichksum. However, if you don't do it on upload with iput -k, there will be no checksum for the TSM ressource.

As mentioned above, several small files should be bundled. Nevertheless, you can still extract an uploaded tar archive on the server and index all contained files with the command ibun. Please read its man page for further details (man ibun).

ichmod has several mandatory parameters:

'-r' is a usefull optional parameter for recursive ACL modifications.

Getting data back from the iRODS archive is done via iget.

1. Get your kerberos ticket and print some information about your iRODS account

2. Navigation

3. Archiving, retrieving files and simple information

4. Checksum

Metadata is defined as so called AVU triplets (Attribute, Value, Unit). The first two fields (AV) are mandatory and must not be empty, the unit is optional. AV are defined as VARCHAR(2700) and U as VARCHAR(250), which means they are all text with a maximum size of 2700 and 250 characters, respectively. They might also contain JSON, XML or YAML as text.

Command Description:

The following command lists the metadata automatically associated with the previously upladed file hello_world.txt:

imeta ls -d hello_world.txt

The output of the query is:

AVUs defined for dataObj hello_world.txt:
attribute: AccessRights
value: closed
units: 
----
attribute: Creator
value: Steinkamp, J.
units: 
----
attribute: Date
value: 1566206896
units: 
----
attribute: ExpiryDate
value: 1882430896
units: 
----
attribute: Location
value: Mainz, Germany
units: 
----
attribute: protected
value: false
units: 
----
attribute: Publisher
value: Johannes Gutenberg-University
units: 
[user@login01 ~]$ 

You can now add a title, which is not created automatically:

imeta set -d hello_world.txt Title "Archive of experimental szstem from '$(date)'"

If you query the Attribute 'Table' with imeta ls -d hello_world.txt Title you get:

AVUs defined for dataObj hello_world.txt:
attribute: Title
value: Archive of experimental szstem from 'Mon Aug 19 11:39:48 CEST 2019'
units: 

$ imeta mod -d <filename> <attribute> <old value> v:<new value>

imeta mod -d hello_world.txt Title "Archive of experimental szstem from 'Mon Aug 19 11:39:48 CEST 2019'" v:"Archive of experimental system from 'Mon Aug 19 11:39:48 CEST 2019'"

As you could see above, we generate as many metadata attributes as possible automatically, to hopefully simplify your life. Nevertheless, you can adjust and extend them to your needs.

• Set automatically:
  • Creator full user name
  • Publisher “Johannes Gutenberg-University”
  • Location “Mainz, Germany”
  • Date Unix timestamp
  • ExpiryDate Date + 10 years
  • protected (default: “false”)
• User input required:
  • Title free text
  • Description text
  • Type audio, data set, image, source code, …
  • Format simply the file format (e.g. output from *file* command)
  • AccessRights “closed”, “restricted”, “embargoed”, “open” (default: “closed”)
    • AccessConditions if AccessRights is “resticted” (not yet)
    • EmbargoDate if AccessRights is “embargoed” (not yet)

If the dataset should be FAIR (Findable, Accessible, Interaperable, Reusable) are also mandatory:

• AccessRights must not be “closed”
• Identifier (provided by ZDV/UB, only if attribute “protected” is set; not yet)
• License The license for reuse. Recommended: GPL for code, CC0 for data sets, otherwise CC-BY
• Keywords any keywords

• Contributor co-authors
• Reference publication references

Further fields can be inserted. This depends on the scientific field and is the responsibility of the respective researcher or group.

• general
  • Dublin Core Metadata ( on wikipedia)
  • DataCite
  • https://www.ddialliance.org/Data Documentation Initiative
  • RADAR
  • schema.org
• subject specific
  • Digital Curation Centre

[user@login01 ~]$ ilocate -t "hello_world.txt" 
/zdv/home/user/hello_world.txt
/zdv/home/public/hello_world.txt

You must know, if you want to search for a data object (-d) or a collection (-C). And you can use SQL wildcards (%), if you don't know the exact pattern you are looking for. The wildcard pattern matching is also applicable for ilocate.

[user@login01 ~]$ imeta qu -d Title like "Archive%"
collection: /zdv/home/user
dataObj: hello_world.txt

For this complex syntax consult the Online help.

For public access a ticket needs to be created for collections or data objects. For example, if you use the above uploaded hello_world.txt file again.

[user@login01 ~]$ iticket create read hello_world.txt
ticket:ACR2RKDyuZMBRmb

With this ticket and the path everybody can query information and the content of collections and data objects vi a provided REST-API. JSON strings are returned for valid URLs.

[user@login01 ~]$ curl https://irods-web.zdv.uni-mainz.de/irods-rest/rest/dataObject/zdv/home/jsteinka/hello_world.txt?ticket=ACR2RKDyuZMBRmb

{"id":1808764,
 "collectionId":24346,
 "dataName":"hello_world.txt",
 "collectionName":"/zdv/home/jsteinka",
 "dataReplicationNumber":0,
 "dataVersion":0,
 "dataTypeName":"generic",
 "dataSize":24,
 "resourceGroupName":"",
 "resourceName":"netappResc",
 "dataPath":"/fsapp/iRODS/Vault/home/jsteinka/hello_world.txt",
 "dataOwnerName":"jsteinka",
 "dataOwnerZone":"zdv",
 "replicationStatus":"1",
 "dataStatus":"",
 "checksum":"sha2:XPdR4XQP49lWUGEfPJz0Jo+kmkndGxz6rCQUzCqHteA=",
 "expiry":"00000000000",
 "dataMapId":0,
 "comments":"",
 "createdAt":1566206868000,
 "updatedAt":1566206868000,
 "specColType":"NORMAL",
 "objectPath":""
}

[user@login01 ~]$ curl https://irods-web.zdv.uni-mainz.de/irods-rest/rest/dataObject/zdv/home/jsteinka/hello_world.txt/metadata?ticket=ACR2RKDyuZMBRmb

{"metadataEntries": [
    {"count":1,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"AccessRights",
     "value":"closed",
     "unit":""},
    {"count":2,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"Publisher",
     "value":"Johannes Gutenberg-University",
     "unit":""},
    {"count":3,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"Location",
     "value":"Mainz, Germany",
     "unit":""},
    {"count":4,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"protected",
     "value":"false",
     "unit":""},
    {"count":5,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"Creator",
     "value":"Steinkamp, J.",
     "unit":""},
    {"count":6,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"Date",
     "value":"1566206896",
     "unit":""},
    {"count":7,
     "lastResult":true,"
     totalRecords":0,
     "attribute":"ExpiryDate",
     "value":"1882430896",
     "unit":""},
    {"count":8,
     "lastResult":true,
     "totalRecords":0,
     "attribute":"Title",
     "value":"Archive of experimental system from 'Mon Aug 19 11:39:48 CEST 2019'",
     "unit":""}],
"objectType":"DATA_OBJECT","uniqueNameString":"/zdv/home/jsteinka/hello_world.txt"}

The file content can be viewed with curl or downloaded with wget.

curl https://irods-web.zdv.uni-mainz.de/irods-rest/rest/fileContents/zdv/home/jsteinka/hello_world.txt?ticket=ACR2RKDyuZMBRmb

curl https://irods-web.zdv.uni-mainz.de/irods-rest/rest/collection/zdv/home/public/helloCollection?ticket=mbyAAFGm7vhUdyM

{
 "collectionId":1808781,
 "collectionName":"/zdv/home/public/helloCollection",
 "objectPath":"",
 "collectionParentName":"/zdv/home/public/",
 "collectionOwnerName":"rods",
 "collectionOwnerZone":"zdv",
 "collectionMapId":"0",
 "collectionInheritance":"",
 "comments":"",
 "info1":"",
 "info2":"",
 "createdAt":1566213731000,
 "modifiedAt":1566213731000,
 "specColType":"NORMAL",
 "children":[]
}

the URL for the REST-API consists of:

• Server (https://irods-web.zdv.uni-mainz.de/irods-rest/rest)
• what (collection|dataObject|fileContents)
• iRODS path
• optionally 'metadata'
• Ticket string (?ticket=1234567890)

For further information, please read the original IRODS-REST documentation

The “Creator” is the responsible person in the sense of the Urheberrechtsgesetz, taking care that reusing of third party data is legal and in the sense of the DSGVO, that personal data is handled correctly. Even if the “Creator” is not employed at the university any more.

There exists a decision guide if data can be published, sadly only in german.

Different kinds of Licenses exist for various cases, this here is just an incomplete list of the most common Open Access Licenses for the three most common datatypes:

• Software
  • Apache
  • GPL, GPLv2, GPLv3
  • MIT
  • BSD
• Arts, Images, Text, etc.
  • Creative Commons (Text, Arts, Photos, ...)
• Data sets
  • Open Data Commons

The applicability of CC-BY licenses for Software is not recommended: CC-recommendation and discussion. The same applies for datasets, their publication under a CC-license other than CC0 is doubtful. For other dataset licenses search at Open Definition Licenses Service.

Proprietary file formats should be avoided, since you don't know if the software to open them still exists in a few years. Try to stick to open standards.

There are a lot more commands. You can look them up in the original documentation: iRODS documentation

other wikis:

• CSC.fi
• Technical university of Denmark