heberleh / interactivenn Goto Github PK

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The app uses an outdated library to export files.

It may not work in Safari.

The function saveAs() comes from the old library https://github.com/eligrey/FileSaver.js (npm install file-saver --save)
that can be updated in the code or replaced with a better one.

Here is an example of its use:

saveAs(new Blob([dataset], {type: "text/plain;charset=" + document.characterSet}), document_name);

The code can be slowly migrated from branch dev to Typescript.

In this text, you find a guide with code:
https://medium.com/swlh/convert-your-javascript-react-app-to-typescript-the-easy-guide-631592dc1876

Please use Webpack since we want to be flexible with the settings, that is, don't use create-react-app.

This issue is a piece towards issue #5

Interactivenn was written in poor and simple Javascript.
Many functions are duplicated, etc.

React can be used to manage the state of the App, interactivity and inputs, which in turn call the Services to deal with the data.

Because of flexibility, webpack should be used directly, that is, avoid using create-react-app. This will give us flexibility to generate web and module distributions. I believe it may help in a slow migration to Typescript #7 too.

InteractiVenn is a free tool and widely used by scientists worldwide, counting with many accesses daily.

I welcome any help with improvements in the GUI, code, interactivity or adding new features.

It also has a Help page which would be great for everyone if it's improved.

The tool uses the input boxes as controllers of the data. If the users input data in the boxes, the diagram updates.

However, input boxes have limits: big datasets cannot be copied/pasted or uploaded because the rendering will fail. The browser will get stuck.

A way to contour this problem is to allow upload of bigger files and, if the number of elements is above a threshold, it deactivates the text boxes and only shows the number in the diagram. This means that the text boxes will not display any element.

A mouse-click on a number of the diagrams opens a pop-up with elements in the intersections. This needs to be tested. If it is too much data, it needs to be deactivated too.

A test set has to be prepared, with, for example, 200 MB of data. Maybe some genomes.

Users can download/upload as .ivenn, but it makes much more sense to upload/downlod .xls (Excel) tables since Biologists use that software.

They copy/paste the sets, currently, from a spreadsheet to the InteractiVenn. Then they decide if they want to save the result by downloading the .ivenn.

An option to upload XLS could follow the standard:

• each column is a set
• first row is the set name
• follow rows are elements
• the first 6 columns are parsed into sets (can have fewer columns, can have more, but only up to six are read)
• values in cells must be "trimmed"
• values must be unique (a test must be run and alert a pop-up or show a modal when duplicates are found, and tell users that we ignored duplicates, therefore the total number of elements is smaller than what they find in the spreadsheet)

When users should be informed of important message or new features, a rectangular box could be displayed at the top. Perhaps between the top-bar and the diagram section.

Ideally, once the user clicks [X] (close), the message would not appear anymore for this user (in the same browser).

Perhaps there is already some React library that does the job.

Text box to search for an element, highlighting the right boxes when they contain it.