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handling as URL params instead of JSON #952

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merged 18 commits into from Jan 9, 2018

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nathandunn commented Jan 4, 2018

  • 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 nathandunn self-assigned this Jan 4, 2018

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nathandunn commented Jan 4, 2018

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 nathandunn changed the title from initial foray into handling as URL params to handling as URL params instead of JSON Jan 4, 2018

@nathandunn nathandunn requested a review from enuggetry Jan 4, 2018

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nathandunn commented Jan 4, 2018

@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
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nathandunn commented Jan 4, 2018

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

screen shot 2018-01-04 at 10 50 35 am

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nathandunn commented Jan 5, 2018

@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

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enuggetry commented Jan 8, 2018

It looks good to go. thanks.

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@nathandunn nathandunn merged commit e5584b3 into GMOD:master Jan 9, 2018

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childers commented Jan 10, 2018

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

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nathandunn commented Jan 10, 2018

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

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childers commented Jan 10, 2018

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

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childers commented Jan 31, 2018

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:"}]
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nathandunn commented Jan 31, 2018

@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.

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rbuels commented Jan 31, 2018

@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?

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nathandunn commented Feb 1, 2018

@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.

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rbuels commented Feb 1, 2018

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

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