Add a custom protocol handler for JBrowse Desktop

[garrettjstevens]

There is an example here of how to register an electron app as a handler for a custom protocol. If we regester e.g. the jbrowse:// protocol, we could use a link like jbrowse://something to open JBrowse Desktop from a browser or another app. One use for this could be an "Open in dekstop" menu item in JBrowse Web.

[raj1701]

Hey @rbuels @garrettjstevens can I work on this?
I am planning to make a new main.js file in the src folder of jbrowse_desktop and follow the steps given in the provided link. Is this the right direction?

[cmdcolin]

@raj1701 the code would likely go in this file https://github.com/GMOD/jbrowse-components/blob/main/products/jbrowse-desktop/public/electron.ts

we may not have the bandwidth to help, but if you'd like to try, you can

[raj1701]

Sure I will give it a go. Working on this will give me a better understanding of the codebase atleast.

[cmdcolin]

sounds good. see the short note on the readme here for developing the desktop https://github.com/GMOD/jbrowse-components#quick-start-for-developers specifically I recommend launching two tabs for developing the desktop app.

the yarn electron command essentially runs the electron.ts file that i linked, and then yarn start command starts the webpack watch server that runs the rest of the codebase. you may need to restart the yarn electron command after your changes to the electron.ts file

[raj1701]

Hey @cmdcolin can you please help me with how the electron app is packaged.
Which is the main config file. Is it craco.config.js?
I basically need to enter the declaration of the custom protocol in the config file.

[cmdcolin]

we do not use electron-packager or electron-fiddle, we use electron-builder. can google around but this is the first google result for electron-builder https://stackoverflow.com/questions/45809064/registering-custom-protocol-at-installation-process-in-electron-app

[cmdcolin]

the config for builder may be here https://github.com/GMOD/jbrowse-components/blob/main/products/jbrowse-desktop/package.json#L110

[raj1701]

Thanks @cmdcolin will look into it

[raj1701]

Hey @cmdcolin . I was able to add a custom protocol in windows by adding the following code

• app.setAsDefaultProtocolClient('jbrowse',process.execPath,[path.resolve(process.argv[1])]) in electron.ts
• "protocols": [ { "name": "electron-deep-linking", "schemes": [ "jbrowse" ] } ] inside build of package.json
• run yarn build-electron

After these three the protocol works perfectly in windows but not working in linux.
This shows "electron-userland/electron-builder#4035", something else needs to be tried for linux.
Any insights??

[cmdcolin]

sorry no ideas, but great progress @raj1701 :) that is very cool

[raj1701]

Hey @cmdcolin I tried a lot of things but nothing worked for linux. The problem is no .desktop file is getting created.

It does work perfectly for windows and mac. The above solution does not disturb the linux app. Should I issue a PR for making it work for windows and mac?

Also I wish to apply for GSOC 2023 with jbrowse. Can I pick up some other issue to get familiar with the codebase? Is there some issue you can recommend?

[cmdcolin]

sure thing, you could create a PR for the work so far with windows/mac. the linux 'landscape' might definitely be more challenging, i don't think a .desktop file always can be counted on for example. it might be we could ship the feature without linux support

[cmdcolin]

as far as other things to get familiar with the codebase, it is hard to recommend. there are just not a lot of low hanging fruit hanging out in the issue queue for a long time so even our 'good first issues' are significantly involved in many cases. if you want to just browse the issues and see if any are of interest, post and let us know. can also just try to learn background about genomics, bioinformatics, react, typescript, mobx-state-tree, etc.

[raj1701]

Thanks for the help @cmdcolin. I will look into the topics you mentioned and also the Gsoc idea "BLAST integration for JBrowse 2". Also I was thinking of writing a draft proposal for this idea. For getting reviews can I contact you?

[cmdcolin]

sure thing :) if you are comfortable can post on https://github.com/GMOD/jbrowse-components/discussions or can email me

[raj1701]

Thank you very much @cmdcolin.

[raj1701]

Hey @cmdcolin I have started with an initial draft of the proposal for the idea "BLAST integration for JBrowse 2". Can you please share your email id.

[cmdcolin]

I believe you can submit draft to the gsoc portal now, and I can read it there

[raj1701]

I have submitted the proposal on the portal @cmdcolin. Please review it

[cmdcolin]

as mentioned here there is probably a larger effort involved to open up data in desktop related to loading the same data in the view on web into the view on desktop #3579 (comment) just knowing the basics of protocol handlers that you submitted is useful though

[cmdcolin]

oh sorry I thought you meant to review the PR, you meant the gsoc portal. nevermind above comment

[raj1701]

No problem. Please let me know the changes required in the proposal. I will update it accordingly. Thanks!

[cmdcolin]

see #3476 for nice mockup of how we could link to desktop from web