handling as URL params instead of JSON

[nathandunn]

• handle addBookmarks
• handle addTracks
• handle addStores
  ~~handle addFeatures ~~
• add tests
• handle nested JSON features in addTracks (e.g., styles)
• convert JSON to URL as well
• mention security issues in the index.html
• mention notation changes in the index.html
• update release notes
• update GMOD JBrowse config
• update Apollo hash version to reflect this

[nathandunn]

http://localhost/jbrowse/?data=sample_data/json/volvox&loc=ctgA:1..50001&tracks=DNA,genes&addStore.store1.type=JBrowse/Store/SeqFeature/GFF3&addStore.store1.urlTemplate=http://localhost/volvox.gff3&addTracks.store1.label=genes&addTracks.store1.type=JBrowse/View/Track/HTMLFeatures&highlight=

http://localhost/jbrowse/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A1..50001&tracks=DNA&addStore.store1.type=JBrowse%2FStore%2FSeqFeature%2FGFF3&addStore.store1.urlTemplate=http%3A%2F%2Flocalhost%2Fvolvox.gff3&addTracks.store1.label=genes&addTracks.store1.type=JBrowse%2FView%2FTrack%2FHTMLFeatures&highlight=

[nathandunn]

@deepakunni3 Can you make sure this works? (not sure why you are not in as a reviewer for this one)

In this case I'm using a remote gff as reference.

http://localhost/jbrowse/?data=sample_data/json/volvox&loc=ctgA:1..50001&tracks=DNA,genes&addStore.store1.type=JBrowse/Store/SeqFeature/GFF3&addStore.store1.urlTemplate=http://localhost/volvox.gff3&addTracks.store1.label=genes&addTracks.store1.type=JBrowse/View/Track/HTMLFeatures&highlight=&addBookmarks.bookmark1.start=3000&addBookmarks.bookmark1.end=4000&addBookmarks.bookmark1.ref=ctgA

[nathandunn]

Its using the GFF3 file that comes with volvox, but should work for any set of anything. Also supports bookmarks.

[nathandunn]

@deepakunni3 / @enuggetry I think this does everything I want to do. It still needs some documentation, but I want to merge this first.

It is using this: https://github.com/rhalff/dot-object

I got the npm package to work, but it ended up being wonky (wanted things at src) and the make release test failed.

@childers, I think this would be worth testing internally. I tried to encompass the work-cases you gave me. You can create URLs from JSON, as well. Some of the tests show how:

https://github.com/nathandunn/jbrowse/blob/e87f81a8eab4929ac8826cfcf601b6ca66085b20/tests/js_tests/spec/QueryParamConfigMapper.spec.js

[enuggetry]

It looks good to go. thanks.

[childers]

@nathandunn Thanks, I've been testing this and it does take the parameters as URL params now. This new functionality works great. Thanks!

[nathandunn]

Wait, it works for both JBrowse and Apollo now? (I haven't tested it)

[childers]

The URL params work great in JBrowse, but don't work in Apollo. I can open an issue there if that's helpful. Please see GMOD/Apollo#1840 for some more information

[childers]

I just noticed that addFeatures doesn't seem to be implemented, or if it is, I can't figure it out.

As an example I have a URL with some features here:

https://apollo.nal.usda.gov/Drosophils%20bipectinata/jbrowse/?loc=scf7180000394085:914360..917628&tracks=DNA,Annotations,BlastResults&addTracks=[{"style": {"renderClassName":"blast-hit-20pct"},"label":"BlastResults","store":"url","type":"JBrowse/View/Track/HTMLFeatures"}]&addFeatures=[{ "seq_id":"scf7180000394085", "start": 914360, "end": 914389, "strand": "1", "name": "HSP:"},{ "seq_id":"scf7180000394085", "start": 917599, "end": 917628, "strand": "1", "name": "HSP:"}]

I can get all of the other sections working, but can't seem to work out the addFeatures params.

&addFeatures=[{ "seq_id":"scf7180000394085", "start": 914360, "end": 914389, "strand": "1", "name": "HSP:"},{ "seq_id":"scf7180000394085", "start": 917599, "end": 917628, "strand": "1", "name": "HSP:"}]

[nathandunn]

@childers I have not implemented addFeatures, as I thought the most common use-case would be to use a remote url. I've added it to my list (its a "TODO" https://github.com/GMOD/jbrowse/pull/952/files#diff-cfb6e24963d31803b05b44d42ea77246R86).

You have a pretty simple use-case. I'll see if I can't get it done in the next couple of weeks. If you have time to start the implementation in PR, that would be great, as well, and I can simply help you finish it out.

[rbuels]

@nathandunn can you write a section on this in the JBrowse Configuration guide on the wiki, and note that it is coming out in JBrowse 1.12.4?

[nathandunn]

@rbuels You need anything else on this? I'm going to do some work on supporting addFeatures, as well and I will update the doc further as well. Let me know if anything is with it.

[rbuels]

This looks good to me as is! Thanks for this.