Merge pull request #890 from peer35/yoda2.1

Yoda 2.1 upgrade

Author: Jolien-S

blog/2026-07-20yoda21.qmd

@@ -0,0 +1,19 @@
+---
+title: Yoda 2.1 upgrade
+date: "2026-07-20"
+author:
+  - Peter Vos
+  - Diógenes Cruz de Arcelino
+categories: ["Yoda"]
+---
+The Yoda team has updated the [documentation](/tools/yoda/index.qmd) to reflect changes in the new Yoda 2.1 version ([Release Notes](https://utrechtuniversity.github.io/yoda/release-notes/release-2.1.html)). 
+
+Main changes for researchers:
+
+- [Invitation workflow](/tools/yoda/invitation_workflow.qmd) only for external users.
+- Works with latest version of[GoCommands](/tools/yoda/yoda_using_gocommands.qmd). 
+- Option to [move datasets to the Vault](/tools/yoda/vault_archive.qmd#how-to-submitting-a-data-package-to-the-vault) instead of copying them.
+
+Please note the [Known Issues](/tools/yoda/known_issues.qmd).
+
+During the upgrade new functionality was added to be able to move datasets in the Vault from disk storage to the [SURF Data Archive](https://www.surf.nl/en/services/storage-data-management/data-archive), a form of tape storage. The Yoda team will extensively test this functionality in the coming period. Note that this change is only visible to members of a Datamanager Group.

public/tools/yoda/arch-submit-question.png

@@ -3,16 +3,17 @@ title: Costs and Getting Access
 ---
 
 ## How to request access
-Requesting a project folder in Yoda is done via a 🔒 [request form on ServiceNow](https://services.vu.nl/esc?id=sc_cat_item&sys_id=20436ee397c6a910e553359fe153aff1).Please note that because there can be costs involved (see below) you need to supply a budget code.
+### New projects
+Requesting a project folder in Yoda is done via a 🔒 [request form on ServiceNow](https://services.vu.nl/esc?id=sc_cat_item&sys_id=20436ee397c6a910e553359fe153aff1). Please note that because there can be costs involved (see below) you need to supply a budget code.
 
-Once the project space has been created you can start to invite your collaborators yourself. Note that VU students must 🔒 [connect a token to SURFsecureID](https://services.vu.nl/kb_view.do?sysparm_article=KB0011809) to be able to log in.
-
-### Intake procedure
+#### Intake procedure
 When you work with sensitive data we will always schedule a meeting with you to help you to safely work with your data.
 
 In the form you can also indicate if you would like some help getting started with Yoda. We can either schedule a short
 15 minute meeting to get you started or a longer meeting to have a closer look at your data and help you setting up a workflow.
 
+### Existing projects
+Once the project space has been created you can start to invite your collaborators yourself. Note that VU students must 🔒 [connect a token to SURFsecureID](https://services.vu.nl/kb_view.do?sysparm_article=KB0011809) to be able to log in.
 
 ## Are there costs involved?
 The costs of storing data in Yoda are detailed in the [Research and Archiving Storage Cost Model](https://rdm.vu.nl/topics/cost-model.html). 

tools/yoda/cost_access.qmd

@@ -42,7 +42,7 @@ When in doubt about what type of data you’re dealing with, please consult your
 
 ### What else can I do on Yoda besides Data Storage?
 
-It supports the entire research process from data acquisition to publication. It enables data publication and the associated minting of persistent identifiers (DOIs). It offers support for standardised workflows for the storage and archiving of research data. You can find more information in the [Yoda Topic Page](https://rdm.vu.nl/topics/yoda.html). 
+It supports the entire research process from data acquisition to publication. It enables data publication and the associated minting of persistent identifiers (DOIs). It offers support for standardised workflows for the storage and archiving of research data. You can find more information in the [Documentation](http://rdm.vu.nl/tools/yoda/vault_archive.html). 
 
 ### What is Metadata? And why is it Important when Using Yoda?
 

tools/yoda/faq.qmd

@@ -34,7 +34,9 @@ If you are the group manager of a group, you will be able to add users to the gr
 
 ![Adding user](/public/tools/yoda/gm-adduser.png)
 
-The added user will receive an [invitation](./sram_invitations_eduid_activation.qmd) to join the connected SRAM collaboration. Most users will be able to log in with their own institutional account, if their institute is not connected to SRAM they need to create an **eduID (NL)** account.
+If the user is external (no VU email address) they will receive an [invitation](./sram_invitations_eduid_activation.qmd) to join the SURF Research Access Management (SRAM) _Collaboration_ for external VU Yoda users. 
+
+Most users will be able to log in with their own institutional account; if their institute is not connected to SRAM they need to [create an **eduID (NL)** account](sram_invitations_eduid_activation.qmd#how-to-creating-eduid-throught-sram-invitation).
 
 By default, a new user will be a regular member of the group. If you want the user to be a member with read-only access or
 a group manager, see below for how to change users' roles.
@@ -64,8 +66,6 @@ In order to change the role of a group member:
 
 ![Setting user rights](/public/tools/yoda/gm-role.png)
 
-_Note that you can only change the role of the user after they have accepted the [SRAM invitation](./sram_invitations_eduid_activation.qmd)._
-
 ## How to: Revoking access to a group
 If you are the group manager of a group, you will be able to revoke access to a group in the following way:
 
@@ -80,5 +80,3 @@ If you are the group manager of a group, you will be able to revoke access to a
 6. Click on the red “Remove user” button.
 
 ![Removing user](/public/tools/yoda/gm-removeuser.png)
-
-_Note that you can only remove a user after they have accepted the [SRAM invitation](./sram_invitations_eduid_activation.qmd)._

tools/yoda/group_manager.qmd

@@ -3,17 +3,15 @@ title: Known Issues
 categories: []
 description: Known bugs and issues in the current Yoda version.
 ---
-_Yoda version 2.0_
+_Yoda version 2.1_
 
 | Issue | Description | Workaround | Status |
 | --- | --- | --- | --- |
-| Authentication errors using [Gocommands](yoda_using_gocommands.qmd) version 0.11.x | The 0.11.x versions of Gocommands are incompatible with Yoda 2.0 | Use version 0.10.26 | Expected to be fixed in Yoda 2.1 |
-| Securing datasets in the Vault fails with folders containing special characters | When a datamanager accepts a Vault submission it is copied to the Vault folder. This process sometimes fails if a foldername in the dataset contains special characters (this includes the diaeresis sign, e.g. `ö`). | Ensure folder names do not contain special characters before submitting. | Expected to be fixed in Yoda 2.1 |
-| Connecting using icommands fails due to changes in `irods_environment.json` | Following the Yoda 2.0 upgrade the contents of `irods_environment.json` need to be updated, see [the manual](/tools/yoda/yoda_using_icommands.qmd#environment-file). This is due to an upgrade to the underlying irods system. |  |  |
-| Icon of new user does not reflect role | When a Group Manager changes the role of a recently added user, the icon is not changed. The correct icon will be visible after the user has accepted the SRAM invitation. | Try to change the role of the user again, the system will show a notification stating the user already has this role. | Expected to be fixed in Yoda 2.1 | 
-| Revisions not available | The option to "Search revisions by name" in the Search Bar does not return any results. | If you need to restore an older version of a file from backup please [contact the Research Support Desk](contact_support.qmd) | This feature is intentionally disabled to reduce storage costs. | 
-| _Dataset can be archived and published with a missing ORCID field_ | | | _Fixed in Yoda 2.0_ |
-
+| External users cannot login until they accept a new SRAM invitation | During the Yoda 2.1 upgrade on July 20 2026, all external users received a new invitation by email. They must accept this invitation to be able to login.  |  | This is due to a change in the Yoda-SRAM connection, see [the documentation](sram_invitations_eduid_activation.qmd). |
+| Revisions not available | The option to "Search revisions by name" in the Search Bar does not return any results. | If you need to restore an older version of a file from backup please [contact the Research Support Desk](contact_support.qmd) | This feature is intentionally disabled to reduce storage costs. |
+| _Securing datasets in the Vault fails with folders containing special characters_ |  |  | _Fixed in Yoda 2.1_ |
+| _Authentication errors using [Gocommands](yoda_using_gocommands.qmd) version 0.11.x_ |  |  | _Fixed in Yoda 2.1_ |
+| _Icon of new user does not reflect role_ | _When a Group Manager changes the role of a recently added user, the icon is not changed. The correct icon will be visible after the user has accepted the SRAM invitation._ |  | _Fixed in Yoda 2.1_ |
 
 ::: {.callout-tip}
 The [Yoda release notes](https://utrechtuniversity.github.io/yoda/release-notes/) mention irods bugs relevant to Yoda.

tools/yoda/known_issues.qmd

@@ -10,7 +10,9 @@ If your research project does not have a project space yet, [request it](cost_ac
 Once a project space is created a user with the Group Manager role can [invite colleagues](group_manager.qmd) and set their [access rights](group_manager.qmd#how-to-changing-the-role-of-a-user-in-a-group). 
 
 ### Logging in
-Newly added users receive an [invitation](sram_invitations_eduid_activation.qmd), after accepting they can [login](logging_in.qmd) with their institutional account (VUnetId), with their primary e-mail address as username.
+VU users can [login](logging_in.qmd) straight away after being added, with their primary email address as username. 
+
+Newly added *external* users receive an [invitation](sram_invitations_eduid_activation.qmd), after accepting they can [login](logging_in.qmd) with their institutional account or EduID, with their primary e-mail address as username. 
 
 ## Working With Your Project Space
 A project space is a data folder for storing and organising data during your project. It has a structured name: `research-<faculty>-<department>-<project>`.

tools/yoda/quick_start.qmd

@@ -1,10 +1,14 @@
 ---
-title: SRAM Invitations and eduID Activation
+title: External users - SRAM Invitations and eduID Activation
 categories: []
 ---
 
 To access the Yoda Portal a Single Sign-On (SSO) is required.  Access to a Yoda project is managed through SRAM, where you receive an invitation to join a collaboration. If you are not affiliated with a research or educational institution, you can create a free eduID account. The system will guide you through the process. 
 
+::: {.callout-note}
+Since Yoda version 2.1 VU users no longer need to accept an SRAM invitation to access the VU Yoda instance. 
+:::
+
 You can create an account via the [eduID page](https://login.eduid.nl/request/436c7382-bc00-45f0-b75e-2ede39b49445?lang=en) and use it to log in to SRAM and accept your collaboration invitation.
 
 
@@ -18,7 +22,7 @@ After you are added to a Yoda group by the admin or a colleague you will receive
 
 - If your institute is included in this list and if you are affiliated with a research or education organisation you can choose your institution name which will redirect you to your familiar institutional login page.
 
-- If your institute is not in this list or if you are not affiliated with a research or education organisation please choose **eduID** (NL). If you do not yet have an eduID you can create one for free, the system will guide you through the process. More information on eduID [here])https://login.eduid.nl/request/436c7382-bc00-45f0-b75e-2ede39b49445?lang=en)
+- If your institute is not in this list or if you are not affiliated with a research or education organisation please choose **eduID** (NL). If you do not yet have an eduID you can create one for free, the system will guide you through the process. More information on eduID is available on the [eduID page](https://login.eduid.nl/request/436c7382-bc00-45f0-b75e-2ede39b49445?lang=en)
 
 ![SRAM login with eduID](/public/tools/yoda/sramlogineduid.png)
 

tools/yoda/sram_invitations_eduid_activation.qmd

@@ -48,6 +48,13 @@ you want to submit to the vault. Check that all mandatory metadata has been ente
 ![Submit](/public/tools/yoda/arch-submit.png)
 
 If any mandatory metadata is missing, the system will tell you what metadata still needs to be entered.
+
+You will be presented with a choice to copy or move the dataset:
+
+![Submit, copy or move](/public/tools/yoda/arch-submit-question.png)
+
+If you are not planning to work further on the dataset after archiving/publication, choose move. Note that you can always copy the dataset back from the Vault to Research space later.
+
 If all required metadata is present, the system will lock the folder and its subfolders during the archiving process. This ensures that data in the folder can no longer be changed. Once the system has copied all data to the vault, the lock will be removed
 automatically.
 

tools/yoda/vault_archive.qmd

@@ -20,15 +20,6 @@ This will download the gocmd executable to your current working directory.
 
 Check the [Readme](https://github.com/cyverse/gocommands?tab=readme-ov-file#download-pre-built-binary) for instructions on other platforms.
 
-:::{.callout-warning}
-The current 0.11.x version of Gocommands is not compatible with Yoda 2.0. Please use the [0.10.26](https://github.com/cyverse/gocommands/releases/tag/v0.10.26) version for now. 
-
-Download and zip it manually or adjust the command like this:
-```cmd
-curl -L -s -o gocmd.zip https://github.com/cyverse/gocommands/releases/download/v0.10.26/gocmd-v0.10.26-windows-amd64.zip && tar zxvf gocmd.zip && del gocmd.zip
-```
-:::
-
 ## Configuring the Gocommands
 Before you can start using the Gocommands, you need to set up your environment to connect to Yoda by creating an `irods_environment.json` file. If you already have an `irods_environment.json` file there is no extra configuring to be done, and you can start using commands with the GoCommands immediately.