Recommend looking at synonyms.txt in IGB.
attn: Nowlan Freese

I have updated the species.txt endpoint of the hub API to better translate UCSC organism names into IGB species names.

Please see my changes here.

These changes involve:

• First attempting to derive an IGB species name from, given a UCSC genome version.
• If the above fails, default to using the track hub organism name as the IGB species name.
• If track hub genome contains no organism information, give the genome a tentatively named umbrella species name of 'Trackhub misc'.

In the case of the genome described in this issue, however, neither it nor its provided organism name map to the default/global IGB synonyms.txt or species.txt. Therefore, based on my changes, the genome shows up under the species name of ''thale cress". To get it to show up under the expected IGB species Arabidopsis thaliana, either "thale cress" needs to be added to the global species.txt, or "araTha1" needs to be added to the global synonyms.txt. Only one of this additions is required for these changes to allow for the correct placement of this genome under the appropriate species.

Did code review only, not functional review. Will assess functionality during testing phase.

Philip Badzuh - Please submit PR.

Please see PR here.

Merged and deployed to testing sites.

The bug appears to be persisting as the data source mentioned above is not visible.
I attempted to view data from the following URL by adding it as a data source. But when I visited the genome version for Arabidopsis by clicking on the image on the home page (which is the latest available) I did not see the data source appear.

https://translate.bioviz.org/rest_api/?hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&fileName=/

The host translate.bioviz.org is up-to-date with the latest track hub facade code.

Did you make the changes I describe near the end of this previous comment?

Sorry, I did not. Working on it.

Build and ran new version of IGB from this branch: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2911?dest=master

Adding the new synonym enables IGB to access the JASPAR track hub. However, all the data files appear to load extremely slowly, even when I zoom in and click "Load Data" for a smaller region.
I tried downloading one of the files directly onto my computer, and it will take probably around 15 minutes or longer for the file to download.
(This is the file URL: http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb)
Is the "bigbed" format being handled the way it should in IGB, with the index from the top of the file getting loaded first followed by a second request to retrieve precisely the data needed? Will make a separate issue for this. For now, will merge in the new synonym update to the main development branch and move this ticket to closed.

Merged into IGB master branch (POM version 9.1.10). Moving to Done.