oluwadarelab / robin Goto Github PK

description. Since higlass is somewhat heavy, we should give the users an option to disable it all together if they do not need it for their project, since this will save us some compute time for those who do not need higlass.

Add a toggle button, with a default "ON" state, in the job creation page IE: oneStepJobCreationPage.tsx

description: The home page description needs to be updated.

it can be updated here:
https://github.com/OluwadareLab/Robin/blob/e2a6a426def367b7c09c45bb0f718894f9fd6ae3/src/config.mjs#L14C5-L15C101

jobs will break without atleast 2 results, both of the same resolution.

Overview: If a user leaves the upload page or accidently reloads or loses connection they should not have to reenter all their info

Story:
As a user, when uploading my data to the upload page, when I have to reload the page or get disconnected for any reason then when I come back to the page my data should still be there

Good path:
Given: the user has filled out some of the upload form
When:
1: the user reloads the page
2: the data should still be there

Dev Notes (Mattie):
I implmented about half of this solution inside of the oneStepUploadPage:

Description:
A user should be able to upload their own matrix file to our server and injest into higlass, note: these files are very large so we will only cache them for a short time before deleting them. Discorage the user from using this option and ensure they know to use it as only a last resort if higlass's api does not have ANY data that would work for them

ONLY .cool files allowed. since higlass's clodious data prep script only has multithreading for injesting cool files we will only allow cool file uploads to reduce processing time.

Description:

on the overlap page, the resolution dropdown will display under the "select tools to visualize" active selections it should display on top.

Reproduction Steps:
1: goto a job (Ex: http://biomlearn.uccs.edu/robin/results/14)
2: goto overlap tab
3: select a few tools from the list
4: open the dropdown.
5: observe the overlap occuring.

Expected behaviour:
Dropdown should be on top of the things below it when it opens so that the use can see all options and select easily.

Actual behaviour:
the dropdown is below active elements.

Description: On the overlap page of large jobs soon after they complete, there will be missing combinations that do not display.

Reproduction steps:
1; create a large job, I used 11 tools with 4 res each
2: wait for it to complete
3: once completed quickly veiw the overlap tab
4: click on combinations of tools till one shows the error that I coded for this senerio.

Notes: there are multiple reasons why this could occur. Either the job is not actuall correctly saying when its done and there are still some scripts running, if this is the case it is likely that it is waiting for all scripts to start before saying the job is done, so the last 50 scripts will still be running if this is the case.
The other case is that we send a ton of info in the same api call since its all bundled together, and there could be a network issue of some kind.

description: the logo for the browser tab does not load correctly

The already converted .ico file can be found in /src/public and the index.html is also there

description: update the documentation link in config to point to our config site.

you can change it here:
https://github.com/OluwadareLab/Robin/blob/e2a6a426def367b7c09c45bb0f718894f9fd6ae3/src/config.mjs#L60C5-L60C31

description: higlass a lot of the time will not load untill the user presses "reload higlass" and then clicks back to the highglass tab

reproduction step:
1: load a job
2: click on high glass
3: click off high glass and reload the page
4: click back onto highglass
5: wait 30sec atleast
6: observe higlass has not loaded
7: click reload higlass
8: tab back over to higlass
9: it should be loaded again

notes: I think this is due to higlass being ment to cache results and use cookies, but this was broken in the fork I made porting the higlass repo to our version of react.

Description:
Higlass should automatically injest reference files into their respective tracks represented (by default, but editable by user since its higlass) as type: line.

description: the about page needs to be finished.

you can find it here: https://github.com/OluwadareLab/Robin/blob/main/src/pages/aboutPage.tsx
I already set up paths for you so all you need to do is fill out that page.

if you need custom css, create a css file in the pages folder like
/src/pages/aboutPage.css

then inside the page add

import "./aboutPage.css"

and that page will have the css for it isolated to that page not effecting anything else in the site.

The site uses React-Bootstrap, so if you are using boostrap components use their react-bootstrap alternative.
The components you most likely need are:

import { Container, Row, Col, Form, Button, Card, Collapse, Accordion, AccordionBody, NavLink, AccordionItem } from 'react-bootstrap';

<>
<Container>
<Row>
  Row 1
  <Col>
    col 1
  </Col>
  <Col>
    col 2
  </Col>
</Row>
//this is a horisonal rule to just make things look nicer if you want
<hr/>
<Row>
  row 2
</Row>
</Container>
</>

if you choose to use accordians to make collapsable sections see:https://github.com/OluwadareLab/Robin/blob/main/src/components/aiAssistant/aiInstructions.tsx
for an example of how to use them.

Then if you want the format I use for headers on the site you can either import

import { InstructionHeader } from '../misc/instructionHeader';

<InstructionHeader title="your title"/>

If you need to use markdown you may do the following:

import Markdown from 'react-markdown'

<Markdown>
 {`
## Your markdown here as a string

This is all markdown here

`}
</Markdown>

Description

When the user loads into the overlap page, as shown above, it appears as though nothing is there, it should by default select a resolution and a diagram so that the user does not think it is not working.

Reproduction steps:
1: goto a job (ex:http://biomlearn.uccs.edu/robin/results/14)
2: click the overlap tab
3: notice there is no default resolution selected
4: notice there is no default chart displayed

Expected behavior:
both resolution AND the displayed chart should have defaults that load when the page is loaded.

(optional) Ideally save the last selected graph from the user in cookies, this is not hard, but also not needed.

Actual Behaviour:
neither resolution nor chart display render a non empty default state.