Merge branch 'master' into feat/validate-md

docs/04-BRH_overview.md

@@ -14,9 +14,9 @@ Log in here to unlock controlled-access data and workspace access with your cred
 
 [![Screenshot of Login page][img login]{: style="height:100px"}][Login page]
 
-## [**Request study access and link accounts**][Request study access]
+## [**Check Study Access and Authorize External Data Resources**][Request study access]
 
-Check study access, request access, and connect your account to other resources to access all studies
+Check study access and connect your account to other resources to access all studies for which you are authorized.
 
 [![Screenshot showing you can link your BRH credentials to credentials for external data resources][img req access]{: style="height:100px"}][Request study access]
 

docs/07-how_to_check_request_access.md

@@ -18,21 +18,21 @@ Access is displayed as a green box on top of each Study Page.
 
 Note: If you have access but cannot select the study to export to workspace, it is because the manifest is not yet available. Please use API for these cases.
 
-## Linking Access to FAIR enabled Repositories/Resources
+## Authorize to Gain Access to FAIR-enabled Repositories/Resources
 
 BRH securely provides access to data stored on multiple FAIR repositories, resources, and Data Commons.
 
-**Users need to link their account to currently all resources/repositories in order to:**
+**Users must authorize these resources on their account in order to:**
 
-1. *run* Jupyter Notebooks that utilize data stored on various FAIR repositories.
-2. *export* data that is stored on FAIR repositories from the Discovery Page to the Workspaces.
-3. *download* data that is stored on FAIR repositories from the Discovery Page.
+1. *run* Jupyter Notebooks that utilize data stored in various FAIR repositories.
+2. *export* data that is stored in FAIR repositories from the Discovery Page to the Workspaces.
+3. *download* data that is stored in FAIR repositories from the Discovery Page.
 
-In order to link the account to the involved repositories, navigate to the [Profile Page][Profile page] and link the account to relevant commons by clicking on the the respective Refresh or Authenticate buttons as shown below.
+In order to authorize access to these repositories and data commons, navigate to the [Profile Page][Profile page]. Authorize the relevant commons by clicking on the buttons for the relevant commons (e.g., the Refresh or Authenticate buttons in the image shown below).
 
-Access needs to be renewed after 30 days, as indicated after "Status: expires in [..] days".
+Authorization needs to be renewed after 30 days, as indicated after "Status: expires in [..] days".
 
-![Linking access options on the Profile page][img Login other commons]
+![Authorization options on the Profile page][img Login other commons]
 
 
 <!-- Links and Images -->

docs/09-workspace_page.md

@@ -29,11 +29,12 @@ Once users have access to workspaces, use this guide below to get started with a
 
 5. Select the /pd folder. New files or licenses should be saved in the the /pd directory if users need to access them after restarting the workspaces. Only files saved in the /pd directory will remain available after termination of a workspace session.
 
-      ![Screenshot of the /pd folder][img PD folder]
+      [![Screenshot of the /pd folder][img PD folder]{: style="height:400px"}]
 
       * **Attention:** Any personal files in the folder “data” will be lost. Personal files in the directory /pd will persist.
       * Do not save files in the "data" or “data/brh.data-commons.org” folders.
-      * The folder “brh.data-commons.org” in the “data” folder will host the data files you have exported from the Discovery Page.
+      * The folder “brh.data-commons.org” in the “data” folder will host the data files you have exported from the Discovery Page. Move these files to the /pd directory if you do not want to have to export them again.
+      * /pd has a capacity limit of 10GB.
 
 6. Start a new notebook under “Notebook” in the Launcher tab. Click the tiles in the launcher and choose between Python 3 or R Studio as the base programmatic language. *Note: You can open and run multiple notebooks in your workspace. However, the generic, tutorial and nextflow workspace images are currently separate docker images, so there is no functionality to combine them or run nextflow in the tutorial or generic images. This may be available in the future, after further testing and development activities.*
 
@@ -80,7 +81,8 @@ Users can **download** notebooks by clicking "File" - "Download", as shown below
 The following **environments** are available in the workspaces:
 
 * Jupyter Lab
-      ![Jupyter logo][img Jupyter logo]
+
+      ![Jupyter logo][img Jupyter logo]{: style="height:100px"}
 
 The following **programmatic languages** are available in Jupyter Notebooks:
 

docs/13-workspace_accounts.md

@@ -23,19 +23,21 @@ Trial Access is granted for 2 months when you request access to the BRH Workspac
 
 1. Once they have access to the Workspace page, users can request a workspace account by first logging to BRH (#1), going to the Workspace page (#2), then clicking the Workspace Account Manager link (#3). Click "Log in" and "Yes, I authorize" to open the portal in a new tab.
 
-        ![Step by step navigation to open Workspace Account Manager][img open Workspace AM]
+      ![Step by step navigation to open Workspace Account Manager][img open Workspace AM]
 
       *Some STRIDES users may receive an invitation via email to register for an NIH STRIDES workspace account. These users can also click the link in the invitation email to get to the [BRH Workspace Account Manager][BRH Workspace Acct Mgr].*
 
 
 2. In the BRH Workspace Account Manager, users can see their persistent workspace accounts and any available credits or funds in the accounts. If you only have trial access, you will not see any active accounts.
 
       To request a workspace account with a persistent paymodel, click the "Request New Workspace" button.
-        ![BRH Workspace Account Manager page to request new workspace account][img BRH portal request]
+
+      ![BRH Workspace Account Manager page to request new workspace account][img BRH portal request]
 
 
 3. Choose from any of the 3 persistent pay model funding options: a) STRIDES Grant/Award Funded; b) STRIDES Credits; or c) OCC Direct Pay to request a funded workspace account.
-        ![Options for persistent paymodels to fund workspaces][img Request persistent pay]
+
+      ![Options for persistent paymodels to fund workspaces][img Request persistent pay]
 
 ### **OCC Direct Pay** Funded Workspace Account
 
@@ -50,21 +52,26 @@ Funding a workspace account with OCC Direct Pay has 2 major parts:
 
 *Note: It can take up to a month to receive a BillingID if you act promptly to complete each step.*
 
-1. Go to [**https://payments.occ-data.org**][OCC Payment Portal] or click on the Payment Portal link on the OCC Direct Pay tab for the workspace account request form.
-       ![Screenshot showing where the OCC Payment Portal link can be found in the OCC Direct Pay form][img Link to pay Portal]
-2. Create an account for the OCC Payment Portal: Under Create Account, enter your email address and click “Request Token”. *Note: This should be the email address you use to log into HEAL; Direct Pay is not currently compatible with ORCID login. Please monitor this address, as relevant alerts will be sent here.*
+1. Go to [**https://payments.occ-data.org**][OCC Payment Portal] or click on the Payment Portal link (red arrow below) on the OCC Direct Pay tab for the workspace account request form.
+
+      ![Screenshot showing where the OCC Payment Portal link can be found in the OCC Direct Pay form][img Link to pay Portal]
+
+2. Create an account for the OCC Payment Portal: Under Create Account, enter your email address and click “Request Token”. *Note: This should be the email address you use to log into BRH; Direct Pay is not currently compatible with ORCID login. If you already logged in with ORCID to request a workspace account, please log out and authenticate with either the InCommon or Google option. Please monitor this address, as relevant alerts will be sent here.*
 3. You will receive an email with a 6-digit token within a couple minutes of your request. It may go to spam, so watch the Spam folder, as well.
-4. Copy your token from your email. Paste it into the Enter Token field on the OCC Payment Portal. Click Sign In.
+4. Copy your token from your email. Paste it into the Enter Token field on the OCC Payment Portal. Click Sign In. *(Note: You will be asked to enter a token at each log-in.)*
 5. Successful sign-in will open a [Profile page][Payment Portal Profile] for your account on the OCC Payment Portal. When you first create your account on the payment portal, you will not have any access requests.
-       ![Screenshot showing payment portal profle page, showing no access requests at the bottom.][img BRH logo]
+
+      ![Screenshot showing payment portal profile page, showing no access requests at the bottom.][img Pay Portal Profile]
+
 6. Click the “request access” button. The form shown below will open. Complete the form and click Submit.
-       ![Request Access form on OCC Payment Portal][img BRH logo]
+
+       ![Request Access form on OCC Payment Portal][img request BillingID]
 
        For Role, indicate your role within your organization/institution. If you don't have an institutional affiliation, you can put "independent data analyst"
 
 7. Once the form is submitted, a message will appear indicating successful submission. You will also receive an email (again, check spam).
 8. If you return to the [Profile page][Payment Portal Profile] in the OCC Payment Portal now, you’ll see there is an active request in the table at the bottom. Click “Check Status” to view progress on the steps toward final approval and provisioning of your request. You can view what happens at each stage of processing here: [https://payments.occ-data.org/processing-stages/][OCC processing stages].
-9. When you click Check Status, you can see the progress of your request. At first, you will see that they are processing your request (indicated by an orange color). Once OCC finishes processing your access request, you will receive 2 emails, and the progress tracker at the bottom will show that Submit Access Request is completed (green). Complete E-Doc is now colored orange. The first email indicates that your access request status has progressed, and the second email has a link to an electronic document.
+9.  When you click Check Status, you can see the progress of your request. At first, you will see that they are processing your request (indicated by an orange color). Once OCC finishes processing your access request, you will receive 2 emails, and the progress tracker at the bottom will show that Submit Access Request is completed (green). Complete E-Doc is now colored orange. The first email indicates that your access request status has progressed, and the second email has a link to an electronic document.
 
       >>>
       **Important: Review the Agreement carefully to understand the terms.**
@@ -83,7 +90,7 @@ You may now use your BillingID to provision a Direct Pay workspace account in BR
 
 #### Use BillingID to provision Direct Pay funds for the Workspace Account
 
-*Note 1: Before you request a workspace account through any persistent pay model (eg, Direct Pay, STRIDES), be sure to backup all data in your `/pd` for your workspace. Once your persistent pay model is funded, you will no longer have access to the `/pd` used during blanket billing. ([What’s a `/pd`?][pd link])*
+*Note 1: Before you request a workspace account through any persistent pay model (eg, Direct Pay, STRIDES), be sure to backup all data in your `/pd` for your workspace. Once your persistent pay model is funded, you will no longer have access to the `/pd` used during trial access. ([What’s a `/pd`?][pd link])*
 
 *Note 2: It can take up to 12 business days to provision funds from a BillingID.*
 
@@ -98,7 +105,7 @@ You may now use your BillingID to provision a Direct Pay workspace account in BR
       * Indicate whether you have a credit card you are allowed to use to pay for provisioning the workspace account. If your workspace is personal and you have any credit card, the answer will be yes. If your workspace is organizational - make sure you are not using a departmental card or similar without permission.
       * Indicate what role you have as a researcher on this project.
 
-       ![OCC Workspace Account Request form on BRH Workspace Account Manager][img BRH logo]
+       ![OCC Workspace Account Request form on BRH Workspace Account Manager][img Request Direct Pay workspace]
 
 7. Once you submit this form, you will receive an email with the invoice. (It can take up to 5 business days to be sent.) There will be a secure link in the invoice to submit your credit card information and pay the invoice. When you pay the invoice, OCC will apply the funds, create an AWS account for this project’s workspace, and send that information to BRH to provision your account. This can take up to 7 business days after you have signed the form. You will receive an email when your account is set up and ready to be used in your workspace.
 
@@ -169,6 +176,9 @@ NIH-funded researchers with an active NIH award may take advantage of the STRIDE
 [img open Workspace AM]: ./img/open-wkspc-acct-mgr.png
 [img Request persistent pay]: ./img/persistent-paymodel-request.png
 [img Link to pay Portal]: ./img/link-to-pp.png
+[img Pay Portal Profile]: ./img/payportal-profile.png
+[img request BillingID]: ./img/request-billingid.png
+[img Request Direct Pay workspace]: ./img/request-OCC-workspace.png
 
 <!-- Links -->
 [BRH Discovery]: https://brh.data-commons.org/discovery

mkdocs.yml

@@ -8,7 +8,7 @@ nav:
     - Quickstart - BRH Overview: 04-BRH_overview.md
     - Workspace Page (Registration): 05-workspace_registration.md
     - Login Page: 06-loginoverview.md
-    - Request Study Access and Link Accounts: 07-how_to_check_request_access.md
+    - Check Study Access and Authorize Resources: 07-how_to_check_request_access.md
     - Discovery Page: 08-discovery_page.md
     - Profile Page: 10-profile_page.md
   - Workspace User Guide: