Track ID for per-track indexing

[cmdcolin]

Discussed in #2339

^{Originally posted by bbimber September 16, 2021}
I have a jbrowse 2 session where my config contains a GFF track. This track was indexed standalone using "jbrowse text-search --file xxxx.gff". When I type into the search box i get the expected typeahead. When I pick a feature and the dialog pops up, i get:

The results are valid, but is there a reason track is "N/A"? I'm guessing maybe this has something to do with aggregate indexes (which need to be aware of track), and per-track indexes? The code must "know" the track for these results though?

[teresam856]

The show track button will be disabled if the track does not exist or can't be found. If the index was created using the --file, it could be that the trackId or for this file (the filename as a trackId) is not found.

[teresam856]

If the track had been indexed with --perTrack, then I believe there should be no issue with the trackId. Because the --file has no relationship to an existing track nor does it create a new one when we index that file, then we only use the fileName as the default value for the trackId.

[teresam856]

This is most likely outdated.

[cmdcolin]

@bbimber commented on this

OK. Adding code to retrofit trix xi files as they are made is workable for us. i'll see if this works. It is was possible to support something in jbrowse in future releases to either make the command-line tool specify a track ID, or probably better yet to let the searchConfig in the jbrowse JSON specify the trackId as it exists in the trix index, that would be appreciated

one main issue that he ran into is when using --file, it is not possible to customize the --trackId that is outputted into the ix files

[teresam856]

I see, that would be an issue in the text search configuration of a track since a trackId would be created when adding a track and then another placeholder trackId would be created when creating the index.

[cmdcolin]

can be overridden with the --fileId flag in text-index now