JBrowse2 polishing

[abretaud]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

Addressing comments from #7327

"I am wondering if the "Track Visibility" should not be "On when browser opens" by default." -> that's already the default

I'll finish adding gtf support next week

[abretaud]

Green and ready for review :)

GTF can be loaded know, although GFF is probably better for performances and test indexing

I also fixed a bug on synteny data that I hadn't seen in the previous PR

@lldelisle any other things to change?

[lldelisle]

Thanks for the changes. I proposed a new change. Also I am surprised that you use simsize in your test. I would do a compare="diff" and lines_diff is the number of lines that contains the number of lines that contains a dataset code or something that can change from one instance to the other (but this is maybe too much work...).

[abretaud]

Thanks! I've made the help/label changes, it's better indeed :)

For the tests, I used sim_size because there are many history/dataset ids and paths in both xml and json files, that keep on changing on each planemo run, I tried initially to use lines_diff, but it's painful to count the lines, and it will be painful too to update it. While using sim_size with delta=0, I'm quite sure that the json and xml will be exactly like expected, except the fixed-length-random-chunk-of-strings. There was also the idea of using asserts, but I think we'd miss a lot of small potential differences in the output. We'll see in the future if it's convenient or not like that

[bgruening]

You can use the asserts in addition if you like. And for XML we have those fancy asserts: https://docs.galaxyproject.org/en/latest/dev/schema.html#attribute-is

might be also a good assert to have: https://docs.galaxyproject.org/en/latest/dev/schema.html#is-valid-xml

For json as well: https://docs.galaxyproject.org/en/latest/dev/schema.html#has-json-property-with-text

[mvdbeek]

Could you also replace the .get_metadata() function call and use .metadata (a property) instead ?

[abretaud]

Ok, I added the is-valid-xml test, and replaced the get_metadata() call. For detailed json/xml content asserts I'd vote for doing it later as I don't really have the time to do it now