Implementation is done, when testing found out that the API is returning a different value now for the hubUrlPrefix, which we were planning to use to build the hub.txt url. After discussing with Nowlan Freese, we decided to hardcode the prefix url, which would be the genark hub domain for now, and follow up with the UCSC team for more info.

Nowlan Freese here is the context:

The value for the variable hubUrlPrefix in this API (https://api.genome.ucsc.edu/list/genarkGenomes) has been changed from an actual hub domain (https://hgdownload.soe.ucsc.edu/hubs) to some relative path (/gbdb/genark) we were planning to use the original value to build the hub Url for each genome (by adding the hubUrlPrefix to the hubUrl variable present inside the genome object) and use the hub.txt to load the hubs into IGB.

Example hub.txt url built from the API response:
Before the changes: https://hgdownload.soe.ucsc.edu/hubs/GCA/000/001/905/GCA_000001905.1/hub.txt
After the changes: /gbdb/genark/GCA/000/001/905/GCA_000001905.1/hub.txt (this isn’t the actual hub.txt location, which is giving us an issue to load the hub)

May we know why the change occurred? Is it safe to assume https://hgdownload.soe.ucsc.edu/hubs this would be the domain for the genark genomes in the future as well, so that we can hardcode it on our end? Or else is there any other API that can give us the actual domain for the genark hub?

Will change the code to use the hardcoded domain and do the testing again.

Changes are completed and everything's working as expected. Here's the branch that has updated code: https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4088. Please review and let me know if there are any issues.

To test:

1. Pull the branch in your local and build the ucsc-genark-data-provider service using "mvn clean install"
2. Run IGB.
3. Now add the data provider as a plugin in IGB, while choosing the folder choose the generated target folder of the ucsc-genark-data-provider service.
4. Check whether the genark genomes are getting populated or not. (This is the API https://api.genome.ucsc.edu/list/genarkGenomes from where genomes are retrieved)

Tested on Mac using IGB 10.2.0 main branch installer with Sravani's 4088 GenArk branch.

• App loads successfully in IGB, I am able to see the genomes from UCSC GenArk.
• Code looks good.

Ready for pull request.

Raised the PR and merged it to main in my workspace. As this is an app, we wouldn't be pushing it to the Loraine lab workspace yet. We will be doing it once everything's developed. Closing the ticket.