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  • 05:38
    greenkeeper[bot] commented #91
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Colin Diesh
@cmdcolin
after that link loads (takes a bit) it gave me a error decompressing error
Rishu Verma
@rishuverma
Hey @cmdcolin, shall I upload my proposal on GSoC website for you to verify or shall I send that to you as google draft so that I can fix some potential mistakes that might be there?
Colin Diesh
@cmdcolin
@rishuverma I think you can uoload drafts to the gsoc website
If you want to post here you can too
Rishu Verma
@rishuverma
Okay
Scott Cain
@scottcain
dammit. I hate js regular expressions. Why would this not match var matches = dbxref.match(/GeneID:(\d+)/ ) when the contents of dbxref is GeneID:43740568? Live example when clicking on gene in http://dev.wormbase.org:9018/jbrowse/?data=data%2FSARS-CoV-2&loc=NC_045512.2%3A1..29903&tracks=Genes&highlight=
Colin Diesh
@cmdcolin
looks right
var dbxref = 'GeneID:43740578'; console.log(dbxref); var matches = dbxref.match(/GeneID:(\d+)/ ); console.log(matches); if(Array.isArray(matches)) { dbxref=matches[1];}
that passes
something else happenin
Scott Cain
@scottcain
I’m getting dbxref from f.get(‘dbxref’) when there is only one element. Looks like a scalar. Perhaps it is not really?
Colin Diesh
@cmdcolin
check typeof f.get('dbxref')?
it looks like it should be working to me but i can see that ya, gets null instead of a match
Scott Cain
@scottcain
My perl roots are showing—while I certainly should be able to do this with a regex, it’s an easy problem to solve with substring :-)
Scott Cain
@scottcain
Not working much today. I’m quite sure I have vivid-19 today; no breathing issues yet though. The conjunctivitis is messing with my vision so I don’t really want to be reading on a screen too much today. @nathandunn if you don’t mind, please update the container on the covid19 server from dockerhub. Thanks
Robert Buels
@rbuels
@scottcain ouch take care of yourself. we'll take it from here.
Ian Holmes
@ihh
Hang in there Scott. We are all thinking of you. Stay away from screens and take care of yourself.
Nathan Dunn
@nathandunn
@scottcain I’ll do the update
@scottcain is it true you can’t taste?
@scottcain and take care of yourself.
I’m going to research how to automatically push changes to AWS when docker is updated. We do this for other projects.
Scott Cain
@scottcain
My sense of taste seems ok. Thanks for dealing the the server
Nathan Dunn
@nathandunn
No worries.
It is all updated @scottcain
I think they said “loss of smell” https://www.nytimes.com/2020/03/22/health/coronavirus-symptoms-smell-taste.html but who knows
hopefully you’re just regular sick
(but not very sick).
Let me know if the updates look correct
Nathan Dunn
@nathandunn
this is what the AGR is using: https://www.gocd.org/test-drive-gocd/
a proverbial russian docker doll
Scott Cain
@scottcain
Got a weird message in the the jbrowse mailing list moderation queue: JBrower download is very slow,please send to me the new version to my email! That’s the entirety of the message. Should I bother to let it through and ask what they mean? It’s from a 163.com address, which is frequently used by spammers but I think has legitimate users, particularly in China.
Robert Buels
@rbuels
that's strange, but yeah i guess you could email them the release file, i don't see why not
Scott Cain
@scottcain
k
Ian Holmes
@ihh
@scottcain how are you feeling
Scott Cain
@scottcain
@ihh How much detail do you want? I feel better today than yesterday (the conjunctivitis is essentially gone), but that doesn’t make me as optimistic as it sounds like it would.
Scott Cain
@scottcain
A few hours ago, Angela says to me “have you thought about the fact that you’re following exactly the same trajectory as me but you get everything worse?” I thanked her so much for the food for thought. Here’s hoping I don’t need anything stronger than an inhaler in a few days :-)
Ian Holmes
@ihh
@scottcain yes here’s hoping. Thinking of you. Thanks for the updates.
Robert Buels
@rbuels
@scottcain might consider ordering a pulse oximeter from Amazon (cheapish) to make sure everybody’s oxygen levels don’t get too low. I heard that the body can compensate pretty darn well up to a point, and then it starts having bad trouble after a certain threshold
Rishu Verma
@rishuverma
@cmdcolin I have shared my drafted proposal on GSoC website and to you to in private chat, please have a look
Thanks
Scott Cain
@scottcain
@rbuels that’s not a crazy idea, except that I think it would be unlikely to get here in time to be helpful: everybody else in the family has turned the corner and is recovering well, and if I’m going to have breathing issues, that’s likely to start in the next day or two.
Robert Buels
@rbuels
fair enough; we're all rooting for you
Ian Holmes
@ihh
@scottcain yes we are!
Alankrit Gupta
@alankritgupta091099
Hello everyone
I am Alankrit Gupta 3rd year student of IP University. I went through the idealist of the GSoC 2020 and saw the idea "JBrowse 2 - Phylogenetic tree viewer"
I have worked on MERN stack. I have experience in technologies like redux, PWA , Puppeteer, Redis etc.
After going through the idea I think that tree implementation could be done well with D3.js
What else are the prerequisites I need to know about the project???
and How should I get started??
Colin Diesh
@cmdcolin
@alankritgupta091099 that is...kind of a lot of questions
We're an open source genome browser project
We are creating a version 2 of our project with react currently
And we are aiming to support new types of visualizations like phylogenetic tree
So that is our summary. We find that d3 and react often don't play well because d3 is direct Dom manipulation and react is vdom
You can do d3 in react but you have to "fully do the visualization in d3" you can't really mix
We also do not have a server side component to our app it is just client side js