URIError: URI malformed when using "jbrowse text-index"

[abjanssen]

Dear JBrowse2 users,

I've been trying to get our JBrowse2 session up and running, but I'm running into troubles when making the search files.

I'm using jbrowse text-edit to index the tracks, but I'm getting the same error whatever I do (specifying specific tracks).
The command runs up to a certain percentage, and then throws an error " URIError: URI malformed".

I cannot find much about this error online, so instead I'm asking here.

If you require any files to replicate this, please let me know, I can share them if needed.

[cmdcolin]

can you paste a copy of your config.json by chance?

[abjanssen]

I have attached my config.json here.

config.json

[cmdcolin]

actually you don't necessarily need to paste your config.json. it is actually likely a specific GFF3 data entry (column 9 is supposed to be uri or "perecent encoded" for certain characters, but potentially your files might not be following it. if you search your GFF3 files for the "%" character you might find the issue
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#description-of-the-format

we might be able to make a workaround in the jbrowse text indexing for this to avoid a total crash, but it could be worth looking at your files to see if there are any percent encoding issues

[cmdcolin]

and to add on, you can likely fix it on your end if you find the potentially mis-encoded gff3 data to fix it (change it to the percent encoding for example)

[abjanssen]

So it turns out we had a rough "2%C" instead of "%2C" in our manually curated annotation file somewhere.
Thank you for your quick help, and helping me understand this error!