dice.md

# What Is DICE Project?

DICE (Developing Innovation and Creativity in Education) is an international project co-funded by the Erasmus+ Programme of the European Union.

Its main goals are related to fostering innovation and creativity in education.

This project attempts to be a leading initiative that supports educational community to make progress in the field of innovation and creativity through effective, authentic, practical, sustainable actions.
This project has been funded with support from the European Commission.
For more information, see [http://www.diceproject.eu/][b].

**IT4Innovations participates in DICE. DICE uses the iRods software**

The integrated Rule-Oriented Data System (iRODS) is an open source data management software used by research organizations and government agencies worldwide. iRODS is released as a production-level distribution aimed at deployment in mission critical environments. It virtualizes data storage resources, so users can take control of their data, regardless of where and on what device the data is stored. As data volumes grow and data services become more complex, iRODS is serving an increasingly important role in data management, see [https://irods.org/][c].

## How to Put Your Data to Our Server

**Prerequisities:**

We have to be sure about your identity, this will be done throught this steps:

- sign in with your organisation [B2ACCESS][d] , pages requests valid personal certificate (e.g from GEANT) . Account with "Low" level of assurance, will not have access to IT4I zone

- confirm your certificate in browser

![](img/B2ACCESS_chrome_eng.jpg)

- confirm your certificate in OS (Windows)

![](img/crypto_v2.jpg)

- sign to EUDAT/B2ACCESS

![](img/eudat_v2.jpg)

- after successfull login to B2Access,

***For Non IT4I Users***

- please sign in to our [AAI][f] throught your B2Access account. You have to set new password - it is for iRods access.

***For IT4I Users***

- please sign in to our [AAI][f] throught your B2Access account and link your B2ACCESS identity with your existing account. IRODS pasword will be same as your IT4I LDAP password ( f.e. on code.it4i.cz )

![](img/aai.jpg)
![](img/aai2.jpg)
![](img/aai3-passwd.jpg)
![](img/irods_linking_link.jpg)

- contact our support@it4i.cz by mail, we will create your account at our iRODS server.
- ***fill this request on [EOSC-MARKETPLACE][h] - recommended *** or at [EUDAT][l] , please specify requested capacity.
- ![](img/eosc-marketplace-active.jpg)
- ![](img/eosc-providers.jpg)
- ![](img/eudat_request.jpg)

## ***Access to iRods Collection From Karolina***

- access to cluster is must (it4i account)
- iRODS clients are provided as a module on our ***Karolina*** cluster ( Barbora is in progress )
- module irodsfs loads config file for irodsfs and for icommands too
- password to irods is set already, but you can set new at aai.it4i.cz .

***How to mount your collection***

```console
ssh some_user@karolina.it4i.cz
ml irodsfs
```

- now you can choose between Fuse client or iCommands

***Fuse***

```console
ssh some_user@karolina.it4i.cz
[some_use@login4.karolina ~]$ ml irodsfs

irodsfs configuration file has been created at /home/dvo0012/.irods/config.yml
iRODS environment file has been created at /home/dvo0012/.irods/irods_environment.json

to start irodsfs, run:          irodsfs -config ~/.irods/config.yml ~/IRODS
to start iCommands, run:        iinit

For more information, see https://docs.it4i.cz/dice/
```

To mount your iRODS collection to ~/IRODS, run

```console
[some_user@login4.karolina ~]$ irodsfs -config ~/.irods/config.yml ~/IRODS
time="2022-08-04 08:54:13.222836" level=info msg="Logging to /tmp/irodsfs_cblmq5ab1lsaj31vrv20.log" function=processArguments package=main
Password:
time="2022-08-04 08:54:18.698811" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main
time="2022-08-04 08:54:18.699080" level=info msg="Running the process in the background mode" function=parentRun package=main
time="2022-08-04 08:54:18.699544" level=info msg="Process id = 27145" function=parentRun package=main
time="2022-08-04 08:54:18.699572" level=info msg="Sending configuration data" function=parentRun package=main
time="2022-08-04 08:54:18.699730" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main
time="2022-08-04 08:54:18.922490" level=info msg="Successfully started background process" function=parentRun package=main
```

To unmount it, run

```console
fusermount -u ~/IRODS
```

- you can work with fuse as an ordinary directory  ( `ls, cd, cp, mv` etc )

***iCommands***

```console
ssh some_user@karolina.it4i.cz
[some_use@login4.karolina ~]$ ml irodsfs
irodsfs configuration file has been created at /home/dvo0012/.irods/config.yml.
      to start irods fs run: irodsfs -config ~/.irods/config.yml ~/IRODS

iCommands environment file has been created at /home/$USER/.irods/irods_environment.json.
      to start iCommands run: iinit

[some_user@login4.karolina ~]$ iinit
Enter your current PAM password:
```

```console
[some_use@login4.karolina ~]$ ils
/IT4I/home/some_user:
  test.1
  test.2
  test.3
  test.4
```

- upload `iput` , download `iget`
- for more help, type `ihelp`

## ***Access to iRods Collection From Other Resource***

- we suppose, you will upload your data from your local pc/vm
- password from [AAI][f]

### You Need a Client to Connect to iRods Server

- There are many iRods clients, but we recommend theese:
- Cyberduck - for windows / mac, GUI .
- Fuse (irodsfs lite) - for linux, cli
- iCommands - for linux, cli .
- for access set PAM passwords at [AAI][f]

### Cyberduck

- download [Cyberduck][i]
- download [connection profile][1] for IT4I irods server
- left doubleclick at this file opens connection

![](img/irods-cyberduck.jpg)

### Fuse

- work with your irods collection like ordinary directory
- this is linux client only, basic knowledge of commandline is neccessary

```console
cd ~
wget https://github.com/cyverse/irodsfs/releases/download/v0.7.6/irodsfs_amd64_linux_v0.7.6.tar
tar -xvf ~/irodsfs_amd64_linux_v0.7.6.tar
mkdir ~/IRODS ~/.irods/ && cd "$_" && wget https://docs.it4i.cz/config.yml
wget https://pki.cesnet.cz/_media/certs/chain_geant_ov_rsa_ca_4_full.pem -P ~/.irods/
sed -i 's,~,'"$HOME"',g' ~/irods/irods_environment.json
```

- edit `~/.irods/config.yml` with username from [AAI][f]

***How to mount your collection:***

```console
[some_user@local_pc ~]$ ./irodsfs -config ~/.irods/config.yml ~/IRODS
time="2022-07-29 09:51:11.720831" level=info msg="Logging to /tmp/irodsfs_cbhp2rucso0ef0s7dtl0.log" function=processArguments package=main
Password:

time="2022-07-29 09:51:17.691988" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main
time="2022-07-29 09:51:17.692683" level=info msg="Running the process in the background mode" function=parentRun package=main
time="2022-07-29 09:51:17.693381" level=info msg="Process id = 74772" function=parentRun package=main
time="2022-07-29 09:51:17.693421" level=info msg="Sending configuration data" function=parentRun package=main
time="2022-07-29 09:51:17.693772" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main
time="2022-07-29 09:51:18.008166" level=info msg="Successfully started background process" function=parentRun package=main
```

***How to put your data to iRODS***

```console
[some_use@local_pc ~]$ cp test1G.txt ~/IRODS
```

It works as ordinary filesystem

```console
[some_user@local_pc ~]$ ls -la ~/IRODS
total 0
-rwx------ 1 some_user some_user 1073741824 Nov  4  2021 test1G.txt
```

***How to stop - unmout your collection:***

```console
[some_user@local_pc ~]$ fusermount -u ~/IRODS
```

### iCommands

- this is linux client only, basic knowledge of commandline is neccessary
- we recommend Centos7, ubuntu 20 is optional

***steps for Ubuntu20:***

```console
LSB_RELEASE="bionic"
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE}  main" \
>   | sudo tee /etc/apt/sources.list.d/renci-irods.list
deb [arch=amd64] https://packages.irods.org/apt/ bionic  main

sudo apt-get update
apt-cache search irods
wget -c \
  http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
  http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \
  http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.10_amd64.deb
sudo apt install \
  ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
  ./python-requests_2.18.4-2ubuntu0.1_all.deb \
  ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
sudo rm -rf \
  ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
  ./python-requests_2.18.4-2ubuntu0.1_all.deb \
  ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
sudo apt install -y irods-icommands
mkdir ~/.irods/ && cd "$_" && wget https://docs.it4i.cz/irods_environment.json
wget https://pki.cesnet.cz/_media/certs/chain_geant_ov_rsa_ca_4_full.pem -P ~/.irods
sed -i 's,~,'"$HOME"',g' ~/.irods/irods_environment.json

```

***Steps for centos***

```console
sudo rpm --import https://packages.irods.org/irods-signing-key.asc
sudo wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo
sudo yum install epel-release -y
sudo yum install python-psutil python-jsonschema
sudo yum install irods-icommands
mkdir ~/.irods/ && cd "$_" && wget https://docs.it4i.cz/irods_environment.json
wget https://pki.cesnet.cz/_media/certs/chain_geant_ov_rsa_ca_4_full.pem -P ~/.irods
sed -i 's,~,'"$HOME"',g' ~/.irods/irods_environment.json
```

- edit ***irods_user_name*** in `~/.irods/irods_environment.json` with username from [AAI][f]

```console
[some_user@local_pc ~]$ pwd
/some_user/.irods

[some_user@local_pc ~]$  ls -la
total 16
drwx------. 2 some_user some_user 136 Sep 29 08:53 .
dr-xr-x---. 6 some_user some_user 206 Sep 29 08:53 ..
-rw-r--r--. 1 some_user some_user 253 Sep 29 08:14 irods_environment.json
```

**How to Start:**

**step 1:**

```console
[some_user@local_pc ~]$ iinit
Enter your current PAM password:

[some_user@local_pc ~]$ ils
/IT4I/home/some_user:
  file.jpg
```

***how to put your data to IRODS***

```console
[some_user@local_pc ~]$ iput cesnet.crt
```

```console
[some_user@local_pc ~]$ ils
/IT4I/home/some_user:
  cesnet.crt
```

***How to download data***

```console
[some_user@local_pc ~]$ iget cesnet.crt
ls -la ~
-rw-r--r--. 1 some_user some_user 1464 Jul 20 13:44 cesnet.crt
```

For more commands, use the `ihelp` command.

[1]: irods.cyberduckprofile
[2]: irods_environment.json
[3]: config.yml

[b]: http://www.diceproject.eu/
[c]: https://irods.org/
[d]: https://b2access.eudat.eu/
[f]: https://aai.it4i.cz/realms/IT4i_IRODS/account/#/
[h]: https://marketplace.eosc-portal.eu/services/b2safe/offers
[i]: https://cyberduck.io/download/
[k]: https://docs.it4i.cz/irods.it4i.cz.crt
[l]: https://www.eudat.eu/contact-support-request?Service=B2SAFE