For anyone interested, here is a link to the jbrowse-jupyter https://github.com/GMOD/jbrowse-jupyter/tree/docs. All feedback is welcomed.
also, the tutorial for ismb says it's not generally used for presenting a specific software https://www.iscb.org/ismb2022-submissions/tutorials
i was also surprised too see a relatively shortlist of tutorials! In previous years, their had been more.
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.
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
i do want to try to make more progress on the pag workshop if possible. i dunno
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.
@bbimber if you have a link that shows what you mean by not autoexpanding it may be useful
11 replies
That screenshot is related to the thread above about autoexpanding LGV
@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
Really wish you could put images in threads. This belongs in the view height thread above
2 replies
https://cyber.gc.ca/en/alerts/active-exploitation-apache-log4j-vulnerability
OICR is issuing an IT alert for this ;; an updating list of affected software found here https://gist.github.com/SwitHak/b66db3a06c2955a9cb71a8718970c592
log4j 1.x which still has a vuln but it is a non default configuration
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)
}
}
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
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. :)
@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.