Please see my changes here.

I have a question about this:

                        if ((urlDomainComponents[urlDomainComponents.length - 1] + urlDomainComponents[urlDomainComponents.length - 2])
+                                .equals(certDomainComponents[certDomainComponents.length - 1] + certDomainComponents[certDomainComponents.length - 2])) {
+                            return true;
+                        }

Wouldn't it be better to first use built-in, default checking provided by the base classes, and then, only if that fails, apply this additional logic to catch situations where a subdomain (e.g., "foo" in foo.example.com) fails to match the common name?

Unfortunately, after trying to find a built-in method for parsing the domain and top level domain of a hostname, I was not able to identify any. The URL class can only provide parsing capabilities to the entire hostname level i.e. including any subdomains via the getAuthority() method documented here.

Philip Badzuh - thank you for looking into it again. Please submit PR.

No problem. Please see PR here.

Merged to master branch. Running master branch pipeline on bitbucket to build windows, mac, linux installers.

Installers built and available from main repository downloads section.
Also, deployed new master branch to bioviz main's "early access igb" page.
Ready for testing, but some instructions are needed on how to test as it's a bit challenging to figure it out from this ticket and its linked ticket(s).
Philip Badzuh: Please provide new instructions on how to test the changes, including:

• description of the bug from the users' perspective
• how to check that the bug is fixed

To test, add the following URL to IGB as a new IGB Quickload data source, using a localhost-deployed trackhub facade site.

http://localhost:8000/api/?hubUrl=https://dashr2.lisanwanglab.org/tracks/DASHR2_hub.txt&filePath=/

Next, attempt to load some of the data files from the Quickload source.

If the bug is still in effect, you will observe IGB reporting "feature is not reachable" style of error as mentioned in the title of IGBF-2964: "Investigate: “This feature is not reachable” error"

I ran trackhub-facade site locally. After trying above URL I got an error. Please see attached screenshot. My guess is URL is incorrect.

Dr [~aloraine] Please provide the correct the URL if its incorrect.

You need to get the URL from Philip Badzuh. (The above URL is from Philip during scrum)

The error that relates to this ticket is specific to the IGB application, so you should:

• Make sure you can add the provided URL as a data source in IGB
• Open a an organism/genome combination supported by the trackhub that defines the URL. In this case, you can try homo sapiens, genome hg38 (the first genome in the IGB dropdown)
• Select and load a file in the available data panel folder associated with the URL.
• Observe that no error popup is shown in IGB.

The warning you observed in your browser results from an issue with the content-type in the response of the endpoint not matching the actual content, but the data is still transmitted - you can use developer tools to confirm or try the same request using postman. This should be fixed in a new ticket as it's misleading, however, it shouldn't block you from testing this ticket.

When I added the above URL as a data source in IGB, I got an error saying 'Following servers are not responding - Trackhub' ( Name of the data source). I was not able to select the species and genome version.

Please check the attached snapshots.

Dr. [~aloraine] Philip Badzuh Please check.

After installing the latest IGB release and enabling the IGB quick load data source, the data from the localhost data source is visible. Please see attached snapshots.

Closing the ticket.