Nowlan Freese
I tried the below scenario with a fork from your repository
1. Create a new account on cyverse https://user.cyverse.org/ upto steps for account verification and setting up password
2. I logged out of the default nowlanf account on http://testingsite.bioviz.org/
3. Tried to login with the new account from 1. It did not throw any error as such.
Attached a screenshot for new account page view after login into bioviz connect
Is there something I missed?

Tested:
Created new account at https://user.cyverse.org/signup
Verified email.
Waited until I received emails stating that Discovery Environment access was granted.
Went to https://www.bioviz.org/connect.html and logged in with new CyVerse credentials.
BioViz Connect loaded the home folder.
Uploaded the two attached files (test.bam and test.bam.bai).
Right-clicked on test.bam and selected analyse > Make coverage graph
Analysis Name: Test1
Output File Name : Test1.bedgraph
Clicked Run Analysis

I was then logged out of BioViz Connect
I then used the initialize user workspace endpoint (https://de.cyverse.org/terrain/secured/bootstrap)
When I logged back in to BioViz Connect, I was now able to run the analysis

So we do need to hit the initialize user workspace endpoint. For some reason the user is unable to run analyses until that endpoint is hit. If the user logs into CyVerse Discovery Environment, the initialize user workspace endpoint is hit, which is why we hadn't run into this issue prior.

I have updated the description with the new information.

Chester Dias - could you take a look at this one next?

sure. Will pick this up next.

Based on the discussion today and after some more trial and error, i decided that the right place to add the user initialisation is after cookies are validated in the cyverse.js file.
I have created the functions but the endpoint does not seem to function as expected
curl -X GET -H "Accept: application/json" -H "Authorization: BEARER <ACCESSTOKEN>" "https://de.cyverse.org/terrain/secured/bootstrap?ip-address=173.95.25.211"

RESPONSE from server was
{"error_code":"ERR_SCHEMA_VALIDATION","reason":{"user_info":

}}

I am not sure for the cause of this error. Command is based on the swager link
https://de.cyverse.org/terrain/docs/index.html#!/bootstrap/get_terrain_secured_bootstrap

Nowlan Freese or Karthik Raveendran Could either of you please check the command once? It does not seem to suggest unauthorized error.

I tried with my IP and the server IP

Chester Dias - I tested the following on the command line on my Mac:

curl -X GET -H "Accept: application/json" -H "Authorization: BEARER ACCESSTOKEN" "https://de.cyverse.org/terrain/secured/bootstrap?ip-address=173.95.25.211"

curl -L -X GET 'https://de.cyverse.org/terrain/secured/bootstrap' -H 'Authorization: Bearer ACCESSTOKEN'

curl -X GET -H "Accept: application/json" -H "Authorization: BEARER ACCESSTOKEN" "https://de.cyverse.org/terrain/secured/bootstrap?ip-address=0.0.0.0"

All of these worked for me. I'm not sure what the error you received is saying, it seems very odd. Let's test this together on Wednesday.

As discussed during the meeting with Nowlan Freese after trying to replicate the issue, It turns out that the token returned during initial login on biovizconnect is not able to retrieve the data from the endpoint https://de.cyverse.org/terrain/secured/bootstrap

but using the token returned from the https://de.cyverse.org/terrain/token does work.

Nowlan Freese Please let me know the response to the mail to the cyverse team on this issue. I will go ahead and add all the code so far to the codebase so all we have to do later would be only to modify some URLs as discussed.

Update from CyVerse:

"This is a strange problem. When the authentication happens via the authorization_code flow, CAS returns the user attributes as arrays of strings even when there’s only one value. When the authentication happens via the password flow, CAS returns single-valued user attributes as strings.

Unfortunately, I haven’t been able to find a way to get the attributes to be returned in the same way for the two different flows, which means that a change to Terrain is going to be required. I’ll make the code change and let you know when it’s ready to go."

The issue has been fixed. The token returned from https://de.cyverse.org/terrain/secured/bootstrap should now work when hitting the /secured/bootstrap Terrain endpoint.

Chester Dias - please move ahead with this issue when you have time.

Please review: https://bitbucket.org/chesterdias/django-cyversedev/branch/IGBF-2576#diff

Code looks good, please submit a pull request.

PR: https://bitbucket.org/nfreese/bioviz-connect/pull-requests/243/igbf-2576

Merged https://bitbucket.org/nfreese/bioviz-connect/pull-requests/243/igbf-2576

Code is deployed on https://bvctest6.bioviz.org.
Karthik Raveendran - please check that the DE initialization workflow is functioning properly. Please test with someone on the team who lacks a CyVerse account. Walk them through the process step-by-step and make note of any problems that are observed.

The DE initialization workflow was tested with two candidates. One candidate registered to Cyverse, verified the account (where you can add a password) and then signed in the Cyverse account. Candidate 2 registered to Cyverse, verified the account but did not sign in the Cyverse account. Both candidate was able to log in to Bioviz Connect without a hitch.

I also noticed that https://bvctest6.bioviz.org did not have "View in IGB" buttons for compatible file types.

Karthik Raveendran - did you test that the user that had not signed in to the CyVerse Discovery Environment was able to run analyses?

Unfortunately, I was not able to get the playbooks to run properly and provision the MySQL database. I tried using the "migrate" option and also the previous method, but neither has worked. Please see: IGBF-2818 (linked issue).
However, it may be possible to assess whether changes to enable DE user workspace creation on first login (this issue) independently from analysis-related functions.