Merge pull request #20 from uc-cdis/main

Add updated Workspace User Guide
uc-cdis · Jul 13, 2024 · df459c2 · df459c2
2 parents b648913 + aed718e
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diff --git a/docs/HEAL_workspace_images.png b/docs/HEAL_workspace_images.png
diff --git a/docs/HEAL_workspaces_flavors.png b/docs/HEAL_workspaces_flavors.png
diff --git a/docs/HEAL_workspaces_nb_download.png b/docs/HEAL_workspaces_nb_download.png
diff --git a/docs/HEAL_workspaces_nb_launcher.png b/docs/HEAL_workspaces_nb_launcher.png
diff --git a/docs/HEAL_workspaces_nb_upload.png b/docs/HEAL_workspaces_nb_upload.png
diff --git a/docs/HEAL_workspaces_pd.png b/docs/HEAL_workspaces_pd.png
diff --git a/docs/HEAL_workspaces_pd_dir.png b/docs/HEAL_workspaces_pd_dir.png
diff --git a/docs/HEAL_workspaces_terminate.png b/docs/HEAL_workspaces_terminate.png
diff --git a/docs/heal_workspace_registration.md b/docs/heal_workspace_registration.md
diff --git a/docs/HEAL_workspaces_nb_save.png → docs/img/HEAL_workspaces_nb_save.png b/docs/HEAL_workspaces_nb_save.png → docs/img/HEAL_workspaces_nb_save.png
diff --git a/docs/platform_workspaces.md b/docs/platform_workspaces.md
@@ -8,7 +8,7 @@ New to Jupyter? Learn more about the popular tool for data scientists on [Jupyte
 
 !!! info
 
-    Workspace access requires authorization. Please contact [HEAL Support](mailto:[email protected]) for more information.
+    To use workspaces, you must first register for workspace access as described on the [Workspace Registration page](./workspaces/heal_workspace_registration.md).
 
 1. After navigating to <https://healdata.org/portal/workspace>, users will discover a list of pre-configured virtual machine (VM) images, as shown below.  
 

diff --git a/docs/reporting-repo.md b/docs/reporting-repo.md
@@ -12,7 +12,7 @@ You can check the HEAL Data Platform to see if we have a data repository selecti
 * Search for your study (e.g., by project number, name, or PI)
 * Find your study in the search results. At the bottom of the study row, there may be multiple color-bordered boxes. If we have your repo selection on the platform, it will appear in one of these boxes (generally the first, but does not have to be). The red arrow below shows an example of a study that selected Dryad as their repository. 
 
-![Screenshot of a study with Dryad listed as a HEAL-compliant repository.](..\img\repo-example.png){: style="height:200px"}
+![Screenshot of a study with Dryad listed as a HEAL-compliant repository.](./img/repo-example.png){: style="height:200px"}
 
 ## My study doesn't show the repository I selected. How can I update that?  
 

diff --git a/docs/vlmd/vlmd_healdata_utils.md b/docs/vlmd/vlmd_healdata_utils.md
@@ -41,7 +41,7 @@ Check (validate) an existing HEAL Data Dictionary file to see if it follows the
 
 ## Using the VLMD Tool in HEAL Workspaces with Python
 
-The VLMD tool has also been preloaded into a HEAL workspace, so that you may use it there instead of downloading it to your local machine. To request access to a workspace, see instructions [here](../heal_workspace_registration.md).
+The VLMD tool has also been preloaded into a HEAL workspace, so that you may use it there instead of downloading it to your local machine. To request access to a workspace, see instructions [here](../workspaces/heal_workspace_registration.md).
 
 Once workspace access has been approved, select the **(Generic) Jupyter Lab Notebook with R Kernel** to get started using the VLMD tool. You can start by uploading your REDCap data dictionary or data file to the persistent drive (/pd). Any data not saved to the persistent drive will be lost when the workspace is terminated. For more information, please see our [documentation on HEAL workspaces](../platform_workspaces.md). 
 

diff --git a/docs/vlmd_submission.md b/docs/vlmd_submission.md
diff --git a/docs/workspaces/heal_workspace_registration.md b/docs/workspaces/heal_workspace_registration.md
@@ -8,7 +8,7 @@ For new users without workspace access, please follow these steps:
 
 1. Login to [the HEAL Data Platform](https://healdata.org/portal/login).
   *Please make a note of your specific login username; this is the username that will have access to workspaces.*
-   
+
 2. Click on the [Workspace tab](https://healdata.org/portal/workspace). 
       ![Screenshot of Workspace Tab button](../img/heal_workspace_tab.png)
 
@@ -24,9 +24,7 @@ For new users without workspace access, please follow these steps:
 
       If you see any other message besides a success message, please reach out to us at [[email protected]](mailto:[email protected]). We may not have received your access request.
 
-5. Users will receive an email notifying them that the request has been received. 
-
-6. Users will receive another email notifying them the temporary trial access request has been approved. They should then be able to access workspaces on the HEAL Data Platform. Please note that the timeline for this approval can be a few business days. If you have not received a response after a few business days, please reach out to [[email protected]](mailto:[email protected]) to check the status of your access request.*
+5. Users will receive another email notifying them the temporary trial access request has been approved. They should then be able to access workspaces on the HEAL Data Platform. Please note that the timeline for this approval can be a few business days. If you have not received a response after a few business days, please reach out to [[email protected]](mailto:[email protected]) to check the status of your access request.*
 
 ## Guidelines for Requesting Extended Access to HEAL Data Platform Workspaces using STRIDES
 

diff --git a/docs/workspaces/heal_workspaces.md b/docs/workspaces/heal_workspaces.md
@@ -51,7 +51,7 @@ Once you have access to workspaces, use this guide below to get started with ana
 
 ![Screenshot for terminating your workspace](../img/HEAL_workspaces_terminate.png){: style="height:200px"}
 
-Further reading: read more about how to download data files into the Workspaces [here](downloading_files.md).
+Further reading: read more about how to download data files into the Workspaces [here](../downloading_files.md).
 
 ## Upload, Save, and Download Files/Notebooks