KR question: Does the same weird thing happen when a user tries to load directly from a URL, e.g., by click-dragging a link into the IGB interface?

Initially the thought was that when track name is left blank in the metadata of a file, the entire link is broken up into tree nodes in IGB Data access. I changed the code to fix that to provide the filename as default for track name. Now the track name is never blank for any files. However, the some files continue to have the same problem despite that. The common thing with these files are that the genome version value is '?' symbol (which is applied when the version is blank or default). When a genome version name that exists in IGB is used as value it works like it should where the filename(or user provided name) is the track name but any other value in version the path breaks up into tree nodes in IGB Data Access. Nowlan Freese Any thoughts on how to navigate this?

I have a hopefully brief request (can wait til next week):

Could you make a comment that lists the localhost URLs being requested by the in-page bioviz connect javascript in the two different cases, after ensuring that the track name is no longer blank?

Also, could you add a link to the branch you are working on / experimenting with, so that we can better understand where this functionality is implemented w/in bioviz-connect code base? Or you could just point us to the relevant file and functions within the file, if that makes better sense.

Version field being empty seems to be the only reason why the path breaks up into nodes in Data Access
eg: For /iplant/home/kraveend91/diseaseDa2d.bed, two links are provided below with two different version values
Link 1: version = A_lyrata_Apr_201
Link 2: version = ?

Link 1 only shows filename in Data Access and Link 2 shows directory structure of the URL. I thought it may be the "?". However, any value other than the versions in IGB generates the problem as shown in Link 3, version = sdfhsdhgsdfhsdfh

I have not push the code yet. But the relevant files and functions are:
cyverse.js - function makeAndOpenIgbUrl: Where the version name is checked if empty or default and assigned ? if true. (If empty, file wont open in IGB)
rightpanel.js- function saveMetaData: On-click function for Save button in Metadata page. I am adding the "trackname -> if empty -> assign filename" functionality here.

Karthik Raveendran - that's a bummer. I can take a look at the IGB bookmark logic and see why that's happening. It doesn't make sense to me why IGB would split the full path because the version is empty. We may need to make a change to IGB.

Edit - I just realized the links are in the previous comment, I will use those.

BookmarkUnibrowControlServlet.java
Line 604 in the loadUnknownData method calls igbService.openURI but does not pass in the trackLabel value (even if it was provided in the bookmark). Compare this to the method directlyLoadFile which passes in the trackLabel when calling the igbService.openURI. Most likely this was an oversight.

The igbService.openURI on line 607 will also need to be changed to to use the sym name. Note that the sym name is an optional field, however, so a placeholder name should be used (the file name) if a sym name is not provided.

Also note that when we test this, both BioViz Connect and Galaxy use this same code.

BioViz Connect is already providing a default track name (the name of the file) and is sending that default track name to IGB. No code changes need to be made to BioViz Connect. The issue is in the loadUnknownData method in BookmarkUnibrowControlServlet.java, which is not using the provided track name from CyVerse.

Closing this issue and creating a new ticket (IGBF-2983) to fix the issue in IGB.