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  • May 26 23:26

    rbuels on rest_data_adapters

    basic rest adapter functionalit… (compare)

  • May 26 20:52
    codecov[bot] commented #2983
  • May 26 20:39
    cmdcolin synchronize #2983
  • May 26 20:39

    cmdcolin on include_target_blank

    Include target blank in output … (compare)

  • May 26 19:04
    jrodiger-lifemine commented #2983
  • May 26 18:22
    cmdcolin labeled #2983
  • May 26 18:22
    cmdcolin unlabeled #2983
  • May 26 18:20
    github-actions[bot] labeled #2983
  • May 26 18:19
    cmdcolin opened #2983
  • May 26 18:19

    cmdcolin on include_target_blank

    Include target blank in output … (compare)

  • May 26 17:32
    adamjohnwright synchronize #2968
  • May 26 17:20
    adamjohnwright review_requested #2968
  • May 26 17:19
    adamjohnwright commented #2968
  • May 26 17:08

    cmdcolin on main

    Add some test delays to avoid f… Additional delay for sequence t… (compare)

  • May 26 17:06
    adamjohnwright synchronize #2968
  • May 26 17:04
    adamjohnwright synchronize #2968
  • May 26 17:00

    cmdcolin on adamjohnwright-add-fasta-header

    Fix config slot name (compare)

  • May 26 16:55
    cmdcolin commented #2968
  • May 26 16:52

    cmdcolin on adamjohnwright-add-fasta-header

    adding headers for both bgzip a… taking async process of fetchin… Adding FASTA header location to… and 10 more (compare)

  • May 26 16:50

    cmdcolin on weird_output

    (compare)

Colin Diesh
@cmdcolin
possibly something like getSession(widgetModel).hideWidget(widgetModel.id)
bbimber
@bbimber
hideWidget(model) works, rather than model.id
Scott Cain
@scottcain
@rbuels @hawrobin @cmdcolin : outreach call? I’m in google hangout
Robert Buels
@rbuels
yep coming
Robin Haw
@hawrobin
Sorry I have a clash today!
Scott Cain
@scottcain
@rbuels @cmdcolin are we really having an outreach call Monday at 9:00am? It’s in my calendar, but I am doubting it.
Robert Buels
@rbuels
Hmm no I don’t know how that got on there
I’ll delete it
Scott Cain
@scottcain
👍
Colin Diesh
@cmdcolin
spotted a jb2 svg export in the wild https://twitter.com/ilyavkirov/status/1467854553563512847
bbimber
@bbimber
Hey - i have a question on plugin config. We have a plugin that lets a user choose a custom coloring scheme. This include a custom renderer. By default, renders support the property 'color1', which can be JEXL to set feature color. Our custom renderer has another simple string property called 'palette'. If palette is non-null, we run code that takes that string, builds a JEXL expression, and then sets color1. This works fine if the user picks that interactively. However, I'd like to hook into somewhere such that if the initial rendererConfig JSON has 'palette', we execute code to set color1 right away. Is there a point where I can hook to add this kind of code?
4 replies
bbimber
@bbimber
Is there a way to remove a default menu item from a VCF track? we are currently adding menu items by overriding trackMenuItems() in a custom VariantDisplay class, but it's not clear whether i can remove default items
7 replies
Another question: our user base seems to have a hard time recognizing the track selector icon (we're using ReactLinearGenomeView). Has anyone encountered this and/or looked into more obvious ways to signal to users what to do? In our case, we load with one track pre-displayed, so there isnt the central 'Open Track Selector' button. For comparison, in JBrowse 1 the side panel was considerably more obvious
3 replies
Teresa Martinez
@teresam856
For anyone interested, here is a link to the jbrowse-jupyter https://github.com/GMOD/jbrowse-jupyter/tree/docs. All feedback is welcomed.
Junjun Zhang
@junjun-zhang
nice!
Robin Haw
@hawrobin
@scottcain @rbuels - do we want to do an ISMB 2022 tutorial? The deadline is monday.
Colin Diesh
@cmdcolin
rob is out on vacay right now just fyi
also, the tutorial for ismb says it's not generally used for presenting a specific software https://www.iscb.org/ismb2022-submissions/tutorials
Robin Haw
@hawrobin
opps, thx @cmdcolin. You are correct, it would be from a data viz or workflow persective. I was just looking over the tutorials from last year and they did not reflect a software demo style.
i was also surprised too see a relatively shortlist of tutorials! In previous years, their had been more.
Colin Diesh
@cmdcolin
i suppose if we want to focus more on jbrowse, probably go for a technology track like the link says
1 reply
Junjun Zhang
@junjun-zhang
anyone knows why we use a particular version of the mst library: "mobx-state-tree": "3.14.1", latest release is 5.1.0
Garrett Stevens
@garrettjstevens
I think it's because we use mobx v5, and mobx-state-tree >=v4 requires mobx v6. There are some breaking changes in mobx v6 and we haven't made it a priority to get things working with that version.
Also, we re-export mobx, mobx-state-tree, react, material-ui, and others for plugins to use, so if we upgrade them we risk breaking plugins. Those breaking changes may have to happen someday, but we'll have to plan for it.
Junjun Zhang
@junjun-zhang
thanks @garrettjstevens in terms of plugin, in the isoform inspector I am trying to use the same major versions of the main libraries as you listed, but still try to make sure it works with newer ones
Colin Diesh
@cmdcolin
docs for the d4 format now say it has some support for static http requests https://github.com/38/d4-format#reading-d4-file-served-by-static-http-server
Robin Haw
@hawrobin
@scottcain @cmdcolin - in view of rob being away, are we still meeting at 1?
Colin Diesh
@cmdcolin
hmm
i do want to try to make more progress on the pag workshop if possible. i dunno
Scott Cain
@scottcain
I’ve had no time this week to work on it unfortunately. AGR and WormBase releases have soaked up all my time, so I’d vote for putting it off
bbimber
@bbimber
Hey - I wanted to re-ask a question from earlier: does anyone have suggestions on coaxing an embedded LGV to make itself full page height? This would both be aesthetically preferable to us (otherwise we just have this white space), and at least in our hands it doesnt reliably auto-expand itself. The user can manually drag to open it, but that's not ideal here. Thanks for any ideas.
Colin Diesh
@cmdcolin
@scottcain @hawrobin ok. i suppose we can skip
@bbimber if you have a link that shows what you mean by not autoexpanding it may be useful
11 replies
bbimber
@bbimber
image.png
That screenshot is related to the thread above about autoexpanding LGV
Robin Haw
@hawrobin
@cmdcolin @scottcain can we meet sometime later next week?
Colin Diesh
@cmdcolin
@hawrobin we have a meeting scheduled again dec 17 if that helps
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