Accessing Yoda
Now that you have access to Yoda, you have your own research group. You are the group manager of this research group, a main folder in which you can store and work with your data. You can also give others access to your data via your research group and collaborate.
There are five ways to access Yoda to work with your files:
- the Yoda web portal
- the Yoda Network Disk
- iBridges (a graphical user interface, Python package and Command Line Interface)
- iCommands (Command Line Interface)
- GoCommands (Command Line Interface)
Which method to access Yoda should you use?
In this table you can find a comparison of the different features for the different methods to connect to Yoda.
| Web portal | Network Disk | iBridges | iCommands | GoCommands |
Access files on local computer | ❌ | ✅ | ✅ | ✅ | ✅ |
Archive and publish data | ✅ | ❌ | ❌ | ❌ | ❌ |
Manage access | ✅ | ❌ | ❌ | ❌ | ❌ |
Suitable for large datasets | ❌ | ❌ | ✅ | ✅ | ✅ |
Graphical User Interface (GUI) | ✅ | ✅ | ✅ | ❌ | ❌ |
Command Line Interface (CLI) | ❌ | ❌ | ✅ | ✅ | ✅ |
Programming interface (API) | ❌ | ❌ | ✅ | ❌ | ❌
|
Add archival metadata to Yoda folder | ✅ | ❌ | 〰 | 〰 | 〰
|
Add own metadata to files and folders | ❌ | ❌ | ✅ | ✅ | ✅ |
For all common operating systems like Windows, macOS, Linux | ✅ | 〰️/ ✅ | ✅ | ❌ | ✅ |
Authentication method | account password | data access password | data access password | data access password | data access password |
Legend: ✅: possible, ❌: not possible, 〰️: in certain circumstances
Using the web portal
The web portal is the only method to arrange who gets access to your data (via the group manager), archive data, publish data and create a data access password. This is not possible via the Network Disk, iBridges, iCommands or GoCommands. In the web portal, you can upload, download, move, copy, delete, rename, and in some cases, preview files. However, if you want to up- or download large amounts of data, the other methods are more suitable.
You log into the web portal via the URL of the web portal of your institution using your email address and account password.
Using the Network Disk
The Network Disk allows you to get access to files stored in Yoda via your local file explorer. This is particularly suitable for small- to medium-sized data. The Network Disk allows you to perform basic tasks related to the data, such as up- and downloading data, creating folders, moving, copying, deleting, and renaming files. When using the Network Disk, we recommend to always check whether the file sizes of the source and the destination match.
Do not use the Network Disk in these cases
We do not recommend using the Network Disk when you work with larger datasets or when datasets need to be continuously up- or downloaded, since the connection to Yoda is not always stable and there are no automatic checks whether the data is transferred correctly (webDAV), which can, in some cases, lead to file corruption. In these cases, we recommend using iBridges or iCommands.
You log into the Network Disk via the network drive link using your email address and a data access password.
iBridges
iBridges is software that was made for researchers with little knowledge of the data management system that Yoda is based on, namely iRODS. iBridges leverages all advantages of iRODS in a comprehensive and understandable way and can be used on all major operating systems. It allows you to:
- perform fast and reliable data transfers for small to very large datasets between Yoda and your local computer, a high-performance computer or a workspace in the cloud;
- add and manipulate metadata for files (“data objects”) and folders (“collections”);
- Stream data: open files in Yoda and work with their content in your compute workflows.
iBridges offers three ways to interact with Yoda:
- using a Graphical User Interface (GUI) without any programming (similar to your file explorer);
- by integrating functions from the iBridges Python package into your code,
- via the command line.
The GUI supports non-programming researchers in executing data transfers and data synchronisations, manipulate metadata and making sure your data is complete and correctly saved. The iBridges python package and the Command Line Interface allow you to also automate data transfers and metadata manipulations.
iCommands
Yoda is based on the open source data management system iRODS. Therefore, you can also interact with Yoda using the iRODS communication protocol iCommands. iCommands give you access to all aspects of iRODS, including data and metadata manipulations, “resources” and “rules”.
iCommands come with a rich variety of actions and parameter settings to adjust the operations fully according to your needs. You will be required to gain a deeper understanding of iRODS and data handling (e.g. check summing). If you decide to use iCommands, you should be comfortable using the command line and be accustomed to reading technical documentation.
iCommands are particularly useful for handling large datasets or interacting with Yoda using scripts. However, iCommands only work on a handful of Linux operating systems, installation requires administrative permissions, and usage requires in-depth technical experience with Linux systems. Therefore, in most cases, we would recommend using iBridges over iCommands.
You log into iCommands via the network drive link using your email address and a data access password.
GoCommands
GoCommands is a command line tool for interacting with iRODS, the data management system that Yoda is based on. It is an alternative to iCommands. Some of its advantages over iCommands include that it does not need to be installed, only downloaded, and that it has better cross-platform support. Many of the commands are similar to the ones in iCommands, but there are also additional commands for ease of user experience.