Swestore-iRODS
Contents
Swestore iRODS
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.
Using Swestore iRODS
Basic information
For basic information on how to apply for storage or how to become a member of an existing project, please check the main Swestore page.
Download and upload data
From the command line
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.
- Please check full and updated documentation at iRODS official Documentation.
- For the command line client, iRODS iCommands, please check iRODS Download page.
- Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at Repository of iRODS packages .
- You can check here an example of iRODS iCommands installation on CentOS 7 from repository.
- You can check here an example of iRODS iCommands installation on Ubuntu 16.04 from repository (the same procedure is valid for Ubuntu 18.04).
- You can check here an example of IRODS iCommands installation on Windows from repository.
- Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at Repository of iRODS packages .
- Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:
{
"irods_host": "irods-login.swestore.se",
"irods_port": 2432,
"irods_default_resource": "pdc-gpfs",
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",
"irods_user_name": "<YOUR_SNIC_USER_NAME>",
"irods_zone_name": "snic.se",
"irods_client_server_negotiation": "request_server_negotiation",
"irods_client_server_policy": "CS_NEG_REFUSE",
"irods_encryption_key_size": 32,
"irods_encryption_salt_size": 8,
"irods_encryption_num_hash_rounds": 16,
"irods_encryption_algorithm": "AES-256-CBC",
"irods_default_hash_scheme": "SHA256",
"irods_match_hash_policy": "compatible",
"irods_authentication_scheme": "PAM"
}
First issue
iinit
which will ask for your iRODS password. You can specify a longer time limit
for the session using the --ttl option, iinit -h --ttl
will print help using this. The default generally will suffice.
Use
ils
just to check if you can access your home directory. Please use the project
directory to store files, which will be a subdirectory under
//snic.se/projects/<SNIC_PROJECT_NAME>.
To transfer data you can use
irsync like:
irsync -v -r -K local_directory i:irods_directory
where
-v for verbose.
-r for recursive copy of the whole directory tree.
-K to compute and check checksums. This involves higher CPU usage
but gives confidence for the integrity of the data stored.
i.e.:
irsync -r -K mydir i:/snic.se/projects/projectdir
If, for whatever reason the transfer had been interrupted the second invocation of the command with the same arguments should pick up and continue from that point.
The ihelp command will print a short description of the iRODS
commands.
From GUI client
Graphical User Interface (GUI) clients are known to work on some operating systems.
Access using WebDAV (map a network drive)
WebDAV endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/
Mac OS X
| Accessing Swestore-iRODS via WebDAV on Mac OS X |
|---|
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files.
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer. |
| This is OS standard WebDAV connection · "Connect to server" function in Finder :
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password. 1.Click the 'Finder' icon 2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server. 3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field. 4.Click Connect. Once the connection is made, you are prompted for your WebDAV username/password. Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop. You can now start adding, editing, deleting files in this directory from the comfort of your computer. |
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via mount_webdav command |
Windows
| Accessing Swestore-iRODS via WebDAV on Windows |
|---|
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files.
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer. |
| How to map the Swestore iRODS to a Windows computer
1. You should have received an email telling you about your Swestore iRODS username 2. We’ll use "s_user" for example 3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account 4. Open “File Explorer” 5. Right-click “Network” 6. Click “Map network drive” 7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures." 8. Click "Next" two times (while choosing "Choose a custom network location") 9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443 10. Enter username and password, e.g. s_user and password 11. You can choose to name your new network drive with something meaningful 11. You should now see the folder mapped to File Explorer!
|
From a web browser
| Davrods is an Apache WebDAV interface to iRODS | |||||
|---|---|---|---|---|---|
| Davrods | Projects | https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/ | To browse private data you'll need to authenticate with your username and password. | This interface is intended as simple directory index interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. | |
| Home | https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/ | To browse private data you'll need to authenticate with your username and password. | |||
| Public | http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/ | This web interface is used to share data with "world" and no authentication is required. NOTE: different port 8888 | |||
| Metalnx | Login | https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/ | To access SNIC iRODS Zone you'll need to authenticate with your username and password. | Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone. | |
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:
Let's assume you want to share your "sharefolder" with your external collaborators
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/ /snic.se/projects/operations/sharefolder: FitSM-0_Overview_and_vocabulary.pdf FitSM-1_Requirements.pdf FitSM_Advanced_Training_SOC_V2.5.pdf FitSM_Advanced_Training_SPD_V2.5.pdf FitSM_Advanced_Training_SPD_V2.5_0.pptx FitSM_Expert_Training_V1.4.pdf FitSM_Foundation_Training_V2.10.pdf FitSM_Foundation_Training_V2.10.pptx FitSM_Foundation_Training_V2.11.pdf FitSM_Guide_Identifying_Services_v1.0.pdf FitSM_Sample_Corporate_SLA_v1.0.docx FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx FitSM_Template_SLA_1.0.docx FitSM_Teplate_Basic_Service_Report_1.0.docx C- /snic.se/projects/operations/sharefolder/README C- /snic.se/projects/operations/sharefolder/test [vitlacil@t04n27 ~]$
- Use Metalnx, web application graphical interface, to change permissions on the folder
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.
See picture:
3. Now you can add read permission to anonymous user. Consider also if you are going to apply it to subcollections and files
4. Now your folder permissions should list read permission to anonymous user
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder
- Use command line interface to change permission on folder
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder
Publish your data
For publishing your data via Swestore iRODS, please get in touch with Swestore support at Swestore Support.
Using Swestore iRODS at PDC
- PDC Support pages for Swestore (iRODS)
- PDC Support pages about Swestore (iRODS) client on PDC transfer node
