MSA viz using Nightingale

[triksi254]

Step 1: Install Dependencies npm i @nightingale-elements/nightingale-msa

Step 2: Create a Wrapper Component New file NightingaleMSAWrapper.js

Step 3: Integrate the Wrapper Component Modify your Outputs component to include the NightingaleMSAWrapper

Step 4: Parse the MSA Data in NewAnalysis.tsx

Step 5: Integrate the Parsed Data into the Outputs Component

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[triksi254]

@vincerubinetti @jananiravi please review and give feedback, thank you

[vincerubinetti]

A couple of things just briefly looking at the code and not testing it yet:

• We're using Bun for package management, so package-lock.json should not be there, and you should install things with bun install instead of npm install
• The code needs to be indented properly, which can be done automatically by running bun run lint in the /frontend directory.
• Stylistically, we're using type instead of interface for type declarations.
• React.FC<NightingaleMSAWrapperProps> type is fine, but to be consistent with the rest of the code base, it should really just be named Props. Then you'd do { sequences, features }: Props. See other components for examples.

It's perfectly okay that you've set it up the way you did, because I didn't provide any guidelines in the issue, but I'll want to make a few architectural changes:

• Move low-level, Nightingale-specific options to within the component, e.g. mouseOverFillColor. We want components to have some options for customization to fit our needs, but mostly they should be simple to use from the outside and handle things automatically.
• For now, instead of adding an example use case to the Outputs.tsx section, let's add it to the Testbed.tsx page with completely fake, generated data, like we're doing with the network visualization component.
• It looks like you're adding some things to the NewAnalysis.tsx page which takes whatever the user has inputted and pass it to the MSA component. I'm not sure if we're doing much visualization of raw inputs... that is, I think the data that will ultimately be passed to the MSA component will be coming from the backend, from analysis results, not something that the user inputted verbatim. However I could be very wrong on this. Even if I am wrong though, I will want to set up a generic way that passes all the raw inputs through to the results page, so that any visualizations we have there can use any of the raw inputs. As such, we don't need the changes to NewAnalysis.tsx yet.

I'll probably have some more comments on Monday.

[vincerubinetti]

@triksi254 If you're able to make the changes I discussed above, please do. If not, I won't be able to get to making the changes myself until next week.

[triksi254]

I am currently working on it. It should be ready tomorrow

On Tue, Oct 15, 2024 at 9:38 PM Vincent Rubinetti @.***> wrote:

@triksi254 https://github.com/triksi254 If you're able to make the changes I discussed above, please do. If not, I won't be able to get to making the changes myself until next week.

— Reply to this email directly, view it on GitHub https://github.com/JRaviLab/molevolvr2.0/pull/32#issuecomment-2414744080, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOAL36Z2HXWVEHJTHDUE5LZ3VOKTAVCNFSM6AAAAABP2UFNPKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJUG42DIMBYGA . You are receiving this because you were mentioned.Message ID: @.***>

[triksi254]

bun run lint test shows the error below bun: File name too long: error: script "lint" exited with code 1

[vincerubinetti]

I'm not able to reproduce that error. Can you provide more info, e.g. which commands you ran, what OS you're using, what other logs (errors or otherwise) did you get?

[triksi254]

$ eslint . --fix && prettier **/*.{tsx,ts,module.css,css,html,md,json,yaml} --write --no-error-on-unmatched-pattern

=============

WARNING: You are currently running a version of TypeScript which is not officially supported by @typescript-eslint/typescript-estree.

You may find that it works just fine, or you may not.

SUPPORTED TYPESCRIPT VERSIONS: >=4.7.4 <5.6.0

YOUR TYPESCRIPT VERSION: 5.6.2

Please only submit bug reports when using the officially supported version.

=============
bun: File name too long: 
error: script "lint" exited with code 1` 
This is the full error. Am using windows 10-64 bit

[vincerubinetti]

Also, this typescript is defining a custom element for nightingale...

declare namespace JSX {
  type IntrinsicElements = {
    "nightingale-msa": any;
  };
}

...but it is overwriting/removing the definitions for all other native HTML elements:

I believe to capture both it should be:

namespace JSX {
  interface IntrinsicElements {
    "nightingale-msa": JSX.HTMLAttributes<CustomElement>;
  }
}

[triksi254]

Thanks, I'll check it out!

On Wed, Oct 16, 2024 at 6:33 PM Vincent Rubinetti @.***> wrote:

Also, this typescript is defining a custom element for nightingale...

declare namespace JSX { type IntrinsicElements = { "nightingale-msa": any; };}

...but it is overwriting/removing the definitions for all other native HTML elements: Screenshot.2024-10-16.at.11.15.21.AM.png (view on web) https://github.com/user-attachments/assets/479bdc62-c8ad-4007-b685-c50449b8cbb4

I believe to capture both it should be:

namespace JSX { interface IntrinsicElements { "nightingale-msa": JSX.HTMLAttributes; } }

— Reply to this email directly, view it on GitHub https://github.com/JRaviLab/molevolvr2.0/pull/32#issuecomment-2417191241, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOAL3YJWF65WRFZXROZIF3Z32BONAVCNFSM6AAAAABP2UFNPKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJXGE4TCMRUGE . You are receiving this because you were mentioned.Message ID: @.***>

[vincerubinetti]

See what I did in this PR for more guidance:

https://github.com/JRaviLab/molevolvr2.0/pull/39