Yoda @ WUR
Yoda is a research data management platform that enables you and your research partners to securely deposit, share, publish, and preserve (large amounts of) research data during all stages of a research project.
How to get started
- Determine who will perform general Yoda management tasks.
To work with Yoda in your research group / business unit / or research project, someone needs to be appointed to manage general aspects of Yoda. This person will receive system rights to create new parent folders, manage users that have access to data, and receive ‘Yoda data manager’ rights to review and approve data archival submissions to the Yoda Vault. These responsibilities can be shared across multiple users within your group. Usually, the data steward of your group would fulfil these tasks, but anyone familiar with best practices in data management can receive the same rights if approved by your group.
Send an email to firstname.lastname@example.org with the following information:
- For which research group or project an account needs to be created.
- Who will perform general Yoda management for the requested account.
- Who the project leader / business unit holder / chair-group holder is (preferably within the cc of the email; as that person will have final responsibility of data within the research group).
- Access Yoda@WUR through the webportal at https://yoda.wur.nl or map Yoda as a network drive using https://data.yoda.wur.nl.
Check https://servicedesk.surf.nl/wiki/display/WIKI/Tutorials+for+Yoda for general information on Yoda usage. If you have any questions regarding Yoda usage or would like a short demo, please contact email@example.com.
Frequently Asked Questions
Can Yoda, being a network drive, serve as an alternative for the M:-drive and/or MS-Onedrive?
What is the storage capacity a user gets on Yoda?
There is no limit, but at 25TB of storage within a category, Data Management Support will contact the chair group / business unit / project to advise on optimisation of Yoda usage.
For more information please email firstname.lastname@example.org.
Will the M: or W: drive be phased out in favour of Yoda?
My upload speed is very slow. Can I use different clients to connect to YODA?
Any stability or speed issues tend to occur on Windows systems (MAC and Linux users will be less affected). You can use different clients when they support the WebDAV connectivity that Yoda uses. We recommend the use of CyberDuck for Windows users. Cyberduck is a free program that offers more upload options and better stability configuration than the native Windows WebDAV client. CyberDuck is available in the WUR software center. Take a look at this link for setting up CyberDuck once installed.
Please note that many other clients do not offer the ability to connect through a network drive (including CyberDuck), you will be using the user interface of that client to upload and download data. Also note, as of Yoda 1.8, the Yoda webportal is greatly improved and allows large data uploads and downloads.
If you are uploading massive amounts of data, then using the command line tool iCommands or the iRODS API (for example in python ) is recommended. As iCommands requires an elaborate set-up on Windows systems (using Windows Subsystem for Linux), please contact email@example.com for more information and to get started with iCommands. If you’re familiar with Linux or python, take a look at https://servicedesk.surf.nl/wiki/pages/viewpage.action?pageId=19824798 or https://github.com/irods/python-irodsclient.
Are different clients better security wise? Is one client more safe than the other?
Can files of Yoda users be searched in the research and vault environment on various criteria such as submittal status or metadata items?
Can the default metadata form be changed?
What is the difference between groups and (sub)categories?
A categoryis atop levelhierarchy, it contains alluserresearch-groupswithin yourYoda environment.Subcategories can be used tofurtherorganise theseresearch-groups. A research-group is a folder that the user sees astop levelfolder / parent folder. Users can only see folders andtheirdataforthe research-groups (read parent folders) that they are a member of. So you can use groups to separate data access for different users.
- research-project-health (parent folder)
- research-project-dekoning (parent folder)
chairgroup-ezo (sub category)
- research-project-zoology (parent folder)
- research-project-flight (parent folder)
- research-project-tailbiting-pigs (parent folder)
- research-project-enriched-vs-barren (parent folder)
- research-project-nabs (parent folder)
- research-project-selection-lines (parent folder)
Note that the 2 example are different ways in using Yoda. In the first example, the costs of Yoda usage are carried by the animal sciences group, in the second example by the ADP chair group. The Yoda costs (and allocation of the first free TB) are carried by the category.
What data classification should I select: Public, basic, sensitive, critical? Can I restrict user access by doing this?
At the moment, the Yoda data classification is just a label in the Yoda system with no technical distinction. All data in Yoda is handled as serious, regardless of the label. However, it is good practice to try and classify data appropriately. For example, ‘Public’ for public data, ‘Basic’ for common projects, ‘Sensitive’ for personal data or data to remain internal, and ‘Critical’ when special types of personal data (religion, sex, etc.) are collected or, for example, company secrets. If you believe you have data with a ‘Critical’ classification, please contact firstname.lastname@example.org to discuss security measures in detail. Note that WUR uses the terms ‘Negligible’, ‘Some’, ‘Serious’, and ‘Disruptive’, which (unofficially) conform to the Yoda terms, respectively, ‘public’, ‘basic’, ‘sensitive’, and ‘critical’.
See also here for a guide on how to classify data using the WUR terms.
What is the Yoda Vault?
How do I approve data to the Vault?
If you have Yoda data manager rights, then it is expected that you approve Yoda Vault submissions. Go to Yoda, sign in, and select in the search bar ‘Search by status’ and select the required status to search for. Any submission requests are now visible. You need to check a submission on:
- whether a good and consistent folder structure is applied.
- whether a good and consistent naming structure is applied.
- whether thorough and elaborate documentation is present that explains the folder structure, data, abbreviations, etc.
- whether the Yoda metadata form is completely and accurately filled in.
- whether non-preferred file formats are used (use in the webportal the button ‘actions’ --> ‘check for compliance with policy’ --> choose ‘DANS preferred formats’).
- whether data is conform best practices in data analysis for your discipline (should conform to commonly used data representation; for example: no spaces in column names, first row in spreadsheets should contain column headers and not the third row, column headers should not be spread over multiple rows, should be consistently named between files, data should be similarly represented between files, etc).
- whether personal data is present and whether they conform to appropriate security measures or whether they are allowed to be stored (for example, are the researchers allowed to store this data, do they have informed consents of participants).
See the appropriate pages at https://www.wur.eu/rdm for more information on documentation, organising files and folders, file formats, and sharing data.
If the submission is evaluated and there are no issues, then you can click in Yoda on the button ‘actions’ --> ‘approve submission’. A of the data will then be transferred to the Vault.