Frontend changes for quickload to trackhub converter
Branch : https://bitbucket.org/lorainelab_udaya/hub-facade/branch/IGBF-4162
Documentation: https://wiki.bioviz.org/confluence/display/igbman/View+IGB+Quickloads+in+UCSC+Genome+Browser

This ticket is currently blocked by IGBF-4192. Once the backend is working then we can go ahead and deploy the front end changes.

Moving to backlog until IGBF-4192 is completed.

Branch : https://bitbucket.org/lorainelab_udaya/hub-facade/branch/IGBF-4162

Modified the existing frontend changes for trackhub to quickload changes and created new changes for the quickload to trackhub converter. Currently using the working example created as refernece for quickload to trackhub converter. Need to change the reference example once the new example is created.

CC : Dr. Nowlan Freese

Testing:
1. Use the reference examples for both the converters and check if the convert button is working properly or not.
2. Follow the instructions provided in the response and check the generated url is working as expected or not.

Brainstorming ideas for the UI: https://docs.google.com/presentation/d/18KF6gA2gxK8b00-lozsKEVsjyEPdjiT-hovigh-9VyM/edit?usp=sharing

Commit : https://bitbucket.org/lorainelab_udaya/hub-facade/commits/d00dea8b7e2990cab2d9c5346362ea9d77a64c19

Cc : Dr.Nowlan Freese

Creating example Quickload that can be used to demonstrate the features of the track hub converter.

1. Go to: https://genome.ucsc.edu/cgi-bin/hgHubConnect?#unlistedHubs
2. Enter the following URL: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/nfreese/trackhubconverter/src/main/quickload&filePath=/hub.txt
3. Click Add Hub
4. Click Arabidopsis thaliana: (null)
5. Enter Chr1:6,955,074-6,955,959
6. Click Search

The only issue I ran into was that when in the original annots.xml (see here for an example) the bam files are within a directory structure and include spaces (the title attribute from QL maps to the UCSC track attribute). UCSC track hubs did not seem to like this and it was only once I got rid of spaces and slashes that it worked correctly.

1. It would be good to handle spaces if possible as there is no limitation within IGB and many of our Quickloads use spaces.
2. Would it also be possible to allow for nesting of files in folders in the UCSC track hub? I can't remember if we discussed this as an option. Many of our Quickloads use files within directory structures.

I am deploying branch IGBF-4162 to dev2025.bioviz.org to facilitate review.

cc: Udaya Chinta, Nowlan Freese, saideepthi jagarapu

Please note that we have not yet introduced the code changes needed to deploy code with updated dependencies, work that saideepthi jagarapu has been doing as part of IGBF-4326.

Note on how to deploy a specific branch from a specific fork:

You just need to include parameters "fork" and "branch" in the inventory file, such as:

dev2025 ansible_host=34.225.101.234 domain=dev2025.bioviz.org secret_key=dldlalkdselcekd igb_repository=https://bitbucket.org/lorainelab/integrated-genome-browser/ igb_branch=main quickload_contents_txt=https://data.bioviz.org/quickload/contents.txt stack=Develop repo=https://bitbucket.org/lorainelab_udaya/hub-facade.git branch=IGBF-4162

[hub_facade_hosts:vars]
ansible_ssh_common_args="-o StrictHostKeyChecking=no"

Udaya Chinta - I'm seeing an issue where when I convert a trackhub to a quickload and then click Add to IGB the URL that is being added to IGB is incorrect.

Nowlan Freese, fixed the issue. Please test the changes.

Tested on https://dev2025.bioviz.org/

UI looks good, able to convert and add a converted track hub to IGB and load data.
Able to convert IGB Quickload and view it in the UCSC Genome Browser.

Ready for PR

PR : https://bitbucket.org/lorainelab/hub-facade/pull-requests/54

Tested the changes in prod. Everything is working as expected.