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  • 13:10
    cmdcolin commented #3129
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    ouyang-lang commented #3129
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    cmdcolin commented #3129
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    carolinebridge-oicr review_requested #2929
  • 12:27
    carolinebridge-oicr review_requested #2929
  • 07:22
    ouyang-lang commented #3129
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    ouyang-lang opened #3129
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  • 01:37
    cmdcolin commented #3094
  • 01:20
    cmdcolin commented #3126
  • Aug 08 23:25
    alexjacobsCDS edited #3126
  • Aug 08 18:49
    codecov[bot] commented #2929
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    codecov[bot] commented #2929
  • Aug 08 18:36
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  • Aug 08 18:36

    carolinebridge-oicr on multilevel-linear-view

    lint (compare)

  • Aug 08 18:32
    codecov[bot] commented #2929
  • Aug 08 18:32
    carolinebridge-oicr synchronize #2929
  • Aug 08 18:32

    carolinebridge-oicr on multilevel-linear-view

    skipping broken tests for now (compare)

  • Aug 08 16:16
    alexjacobsCDS opened #3126
  • Aug 08 16:16
    alexjacobsCDS labeled #3126
Colin Diesh
@cmdcolin
since christmas and new years will basically prevent us from meeting for awhile, would be good if we can flesh out that google doc before that dec 17 meeting
@scottcain @hawrobin maybe we can assign ourselves to one or more of the todo items here https://docs.google.com/document/d/11sEGtgM3pUjJJz0te_IhijbdVjHK_KWVOK2-z9eAMZk/edit#heading=h.7vukgf527z6j
Robin Haw
@hawrobin
sounds good!
Garrett Stevens
@garrettjstevens
image.png
Really wish you could put images in threads. This belongs in the view height thread above
2 replies
Colin Diesh
@cmdcolin
any thoughts on a jbrowse 2 release this week?
Garrett Stevens
@garrettjstevens
I think it would be a good idea
Colin Diesh
@cmdcolin
any blockers?
Garrett Stevens
@garrettjstevens
not that I can think of
Caroline Bridge
@carolinebridge-oicr
Colin Diesh
@cmdcolin
that is a baddy of a bug. i tried to evaluate our apollo codebase for the vuln but i think it dodged a bullet by using an older version of log4j
log4j 1.x which still has a vuln but it is a non default configuration
bbimber
@bbimber
I'm trying to follow an example from one of the plugins, in a .ts rather than js file. Is the following the best solution for typing track.configuration? Without that cast on getContainingTrack(), npm build fails:
      .views(self => {
         const { renderProps: superRenderProps } = self
         const filterMenu = {
            label: 'Filter By Attributes',
            icon: FilterListIcon,
            onClick: () => {
               const session = getSession(self)
               const track = getContainingTrack(self) as IAnyStateTreeNode & { configuration: AnyConfigurationModel }
               const widgetId = 'Variant-' + getConf(track, 'trackId');
               const filterWidget = session.addWidget(
                  'InfoFilterWidget',
                  widgetId,
                  { track: track.configuration }
               )
               session.showWidget(filterWidget)
            }
         }
Colin Diesh
@cmdcolin
that is probably a reasonable thing right now. we could possibly improve the typescript on the function itself to return that
there are cases in the typescript related to configs, getting parent things, etc. that are not perfectly typescripted so just doing best effort and casts is generally ok
Teresa Martinez
@teresam856
Just released the first version of JBrowse Jupyter. https://pypi.org/project/jbrowse-jupyter/ https://github.com/GMOD/jbrowse-jupyter . If anyone in the team would like to be added to both Dash JBrowse and JBrowse Jupyter, let me know and I can add you to the repos on Pypi. :)
Robin Haw
@hawrobin
Wonderful. I will send out a tweet if that’s OK
Teresa Martinez
@teresam856
Awesome, sounds good to me!
Ian Holmes
@ihh
Awesome @hawrobin @teresam856 - please let me know when the tweet is tweeted and I will retweet the tweeted tweet
Elliot Hershberg
@elliothershberg
I will also retweet the tweeted tweet when said tweet is tweeted (just saying)
Teresa Martinez
@teresam856
😂 that's a tongue twister
bbimber
@bbimber
Do features support a tooltip in JBrowse2, like JBrowse 1? i'm specifically interested in SvgRenderer, like VCF tracks.
Ian Holmes
@ihh
@hawrobin just checking in about the tweet from yesterday
Robin Haw
@hawrobin
It just went out
1 reply
bbimber
@bbimber
@cmdcolin you asked above if i could give a live instance of the lack of height expansion we see from LGV. This should be accessible: https://prime-seq.ohsu.edu/home/jbrowse-jbrowse.view?session=mgap. It's loading a fairly small dummy VCF dataset, but it has high feature depth over a very small region. You'll see the track immediately gives a scroll bar, rather than having the overall LGV expand.
Colin Diesh
@cmdcolin
thanks for the example
also, amazing feature detail panel
very cool
regarding tooltip: it can be customized with a jexl callback on the display
example in config to display gene_name attribute from a gff https://github.com/GMOD/jbrowse-components/blob/main/test_data/config_demo.json#L180-L192
5 replies
Colin Diesh
@cmdcolin
and regarding the height expansion, that would probably at some level come back to GMOD/jbrowse-components#534 even if the height of the lgv container was made larger by defau, the individual track containers would need to auto adjust
1 reply
Colin Diesh
@cmdcolin
reminder ....trying out weekly meeting in meet.google.com/okp-hfhs-dyp
@hawrobin just in case you are joining, try that link
Robin Haw
@hawrobin
thanks, just wrrapping up another call
joining now
Colin Diesh
@cmdcolin
not sure i see ya yet
Robin Haw
@hawrobin
I’m asking to join!
The endless scrolling wheel!
Ian Holmes
@ihh
Retweeted the mooted tweeted Jupyter tweet https://twitter.com/ianholmes/status/1471197719385427969?s=20
Robin Haw
@hawrobin
image.png
For a tweet that is barely 4 hours old that’s some serious engagement!!
Teresa Martinez
@teresam856
woah! Yay 🥳🥳🥳
Garrett Stevens
@garrettjstevens
Cool!
Scott Cain
@scottcain
That’s quite cool.
Junjun Zhang
@junjun-zhang
👍👍👍
Robin Haw
@hawrobin
image.png
Seriously, I have to stop doing this……..otherwise you’ll think that I just read twitter all day!
Robin Haw
@hawrobin
All of @ihh data science buddies are probably reading this right now! It’s great work and the tweet is perfectly pitched at data scientists, there’s a detailed short video, and through RTing it’s gettting picked up by a far wider audience than I would have expected after only 6 hours. What would be nice is if we can check how many people are actually checking out the website?
Teresa Martinez
@teresam856
1 reply
Ian Holmes
@ihh
That is really cool @hawrobin cheers for sharing