doc: add api keys section to user guide (#502)

* Add API keys guidance to user guide

* update user guide API keys section

* change headings

* apply suggestions

* remove scenario 1 and 2 text in heading

Author: davidverdu

docs/guide/content/user_guide/api_keys.md

@@ -0,0 +1,54 @@
+# API keys
+
+Some repository features in OnDemand Loop require access to restricted content. API keys let the application request this content — such as draft datasets or unpublished depositions — from services like Dataverse and Zenodo on your behalf.
+
+ Without a repository API key, OnDemand Loop can browse and download only the public versions of datasets that have already been published. Drafts or private uploads remain inaccessible, and attempts to load them from the interface will fail.
+
+---
+
+### Getting your Dataverse API token
+
+1. Sign in to your Dataverse installation.
+2. Click your user name in the top-right corner and select **API Token** from the menu.
+3. If you do not already have a token, click **Create Token**. Otherwise, copy the existing token value.
+4. If you already have a token, check the expiration date. If it has expired, click **Recreate Token** to obtain a new one.
+5. Keep the token secure — treat it like a password. You can regenerate or delete it at any time from the same page.
+
+---
+
+### Getting your Zenodo API key
+
+1. Sign in to Zenodo. 
+2. Open the **Applications** page from the user menu.
+3. In the **Personal access tokens** section, click **New token**.
+4. Enter a descriptive name (for example, `OnDemand Loop`) and select the scopes required by your workflow. For accessing drafts and uploading files through OnDemand Loop, enable at least the `deposit:actions` and `deposit:write` scopes.
+5. Click **Create** and copy the generated token. This value is shown only once; store it securely.
+
+!!! warning
+
+    Zenodo lets you create multiple tokens with different permissions. Remove any tokens you no longer use to reduce risk if a key is ever exposed.
+
+---
+
+### Setting API keys in OnDemand Loop
+
+Once you have the token or key, add it to the corresponding repository connector:
+
+#### The repository exists in Settings
+
+1. In OnDemand Loop, open the **Repositories** drop-down in the navigation bar and choose **Settings**.
+2. Select the repository installation you want to configure (It has been used previously).
+3. Paste your API token in the field provided for that connector.
+4. Click on **Save Changes** to store the credentials securely for the current user account.
+
+#### The repository does not exist in Settings
+
+1. In OnDemand Loop, open the **Repositories** drop-down in the navigation bar and choose **Settings**.
+2. If the repository has not been configured, click on **Add repository** and enter the repository url (for example
+   https://demo.dataverse.org).
+3. Select the repository installation yu have just created.
+4. Paste your API token in the field provided for that connector.
+5. Click on **Save Changes** to store the credentials securely for the current user account.
+
+
+After you save the key, OnDemand Loop can load draft datasets from Dataverse, view unpublished Zenodo depositions, and perform other actions that require authenticated access. You can remove or update keys at any time from the same settings page.

docs/guide/content/user_guide/finding_data.md

@@ -14,7 +14,7 @@ The application supports two ways of finding datasets from remote repositories:
     See the [Supported Repositories](supported_repositories.md) section for the current list. [Contributions to support additional repositories are welcome!](../development_guide/contributing.md)
 
     **Public datasets** with published versions are supported by default.  
-    Access to **unpublished or draft content** may require an API key, depending on the repository's access policies.
+    Access to **unpublished or draft content** may require an API key, depending on the repository's access policies. See [API keys](api_keys.md) for details on how to configure access for Dataverse and Zenodo.
 
 ---
 
@@ -81,6 +81,8 @@ Once a dataset is selected, **OnDemand Loop displays its metadata and file listi
 
     - For **Zenodo** depositions, a registered API key is needed to load any unpublished or draft content.
 
+    - See the [API keys](api_keys.md) section for more details.
+
 #### 3. Reopen Recent Repositories from Activity
 
 You can quickly return to datasets you've already explored:

docs/guide/content/user_guide/supported_repositories.md

@@ -28,13 +28,13 @@ You can find a list of known public Dataverse instances on the <a href="https://
 
 - Download individual files from public or draft datasets.
 - Public dataset versions are available by default. 
-- Draft dataset versions require the presence of an API token.
+- Draft dataset versions require the presence of an API token (See [API keys](api_keys.md) section)
 - Files must be under 10&nbsp;GB in size.
 - Checksums are verified after download.
 
 **Upload**
 
-- Requires a Dataverse API token.
+- Requires a Dataverse API token (See [API keys](api_keys.md) section).
 - Upload to an existing dataset or create a new dataset inside a collection.
 - Files are transferred using the Dataverse API and verified with checksums.
 
@@ -128,10 +128,10 @@ You can access the **Settings** page from the **Repositories** dropdown in the t
 From this page, you can:
 
 - View all previously used repositories.
-- Edit existing API keys.
-- Add API keys for newly used repositories.
+- Edit existing [API keys](api_keys.md).
+- Add [API keys](api_keys.md) for newly used repositories.
 - **Delete repositories** to remove their saved settings.
 
 Deleting a repository clears its associated settings and credentials from the application. This can be helpful for managing outdated or incorrect configurations.
 
-Configuring API keys ahead of time simplifies upload and download operations, particularly when working with draft datasets from platforms like **Dataverse**.
+Configuring [API keys](api_keys.md) ahead of time simplifies upload and download operations, particularly when working with draft datasets from platforms like **Dataverse**.

docs/guide/content/user_guide/uploading_files.md

@@ -15,6 +15,7 @@ Uploads are organized into **upload bundles**, which group a set of files and li
    Each upload bundle requires an API key for authentication.
     - If no key is present, a red badge appears in the bundle header.
     - Click the **pencil icon** to enter your key and choose whether to save it globally or only for this bundle.
+    - Another way of defining the API key is on **Repositories -> Settings** as it is described in [API keys](api_keys.md) section.
 
 3. **Select or Create a Dataset**  
    Depending on the type of URL provided and the rules of the remote repository,  

docs/guide/mkdocs.yml

@@ -27,6 +27,7 @@ nav:
       - Introduction: user_guide/index.md
       - Projects: user_guide/projects.md
       - Finding Data: user_guide/finding_data.md
+      - API keys: user_guide/api_keys.md
       - Downloading Files: user_guide/downloading_files.md
       - Uploading Files: user_guide/uploading_files.md
       - Upload File Selector: user_guide/upload_file_selector.md