It is important that the test cases and even some "production" tools are self-contained. Because some of the testcases require big data set (like the distance matrix of IR spectra) it would be nice to be able to attach directly to a view. This would allow for example to create small database of reference molecule (project of Cyril) or demonstration of the NMR 1D auto-assignment (project from Andres). Would be nice that when you click on a specific view there is a button next to "Make public" that opens a dialog that allow to upload / rename / delete files. Should we consider folders (consequence for couch and URL to retrieve the document) ? It should be feasible because we used them when we were adding the visualizer directly in couchDB. What kind of project could we do with this kind of approach ? Infra-red spectra are around 100kB in jcamp format. If we should consider having 1000 attachments and that the system works correctly with 1000 attachments. This means the document with the attachment would have around 100Mb. We had some trouble with couchDB when we were adding the visualizer directly in the database but we still had more documents in this case.

• https://wiki.apache.org/couchdb/HTTP_Document_API#Attachments
• http://elegantcode.com/2009/07/10/adding-attachments-to-documents-in-couchdb/

We need to put some order in the basic available modules.

In order to change the file system we need to change the way a module is defined. Currently

"Server interaction": {
        "button_url": "Button URL",
}

Each module must include the URL of a folder (relative or absolute) that MUST contain controller.js, model.js and view.js

We could actually think about a 4th file, config.json which contains all the config currently in the controller. Would make a lot of sense then to parse it and create an automatic documentation.

When replacing an existing spectrum for which minY / maxY are different the vertical axis value does not change (or at least is not redraw). If you change again the data the axis value of the previous spectrum is displayed.

Testcase: http://visualizer.epfl.ch/tiny/Y00J8B5uYgBBbRytid1a (Original URL)

https://visualizer.epfl.ch/tiny/LRthDGHoewaR9y146jTa

If you look at this view the spectra looks correct.

Now change the last value of the array

var peak = [1,1,5,1,4,2];

(2 instead of 1)

The peaks are now combined.

But if you force the Y axe this does not happen

You can zoom correctly in the spectra displayer. In the last version the spectrum disappear.

Testcase: http://visualizer.epfl.ch/tiny/P6EzbVQx0wk76IIZpDaU (Original URL)

When zooming in markers don't disappear

ALso the legend shows chart and chart-1, when there is only chart

Testcase: http://visualizer.epfl.ch/tiny/tf5x2M5PprvWn1ttJVE7 (Original URL)

Once I change of layer, I could neither move nor resize any module in the view.

Testcase: http://visualizer.epfl.ch/tiny/THmIvQGa6mJfV9Q4bHrN (Original URL)

Don't understand why the horizontal axe legend is not being displayed in the view:

(just draw anything and click Calculate spectrum)

In the preferences it should be 'δ (ppm)'

It seems that when the input variable is jcamp the label is not set but only in the case of chart. Should not label not be added independently of the input variable kind ?

I have problems to select elements in the view manager menu, because at 100% zoom, the menu appears above the project list. Why this happens? Zoom 100% Zoom 65%

Hey @targos, I implemented a basic method to allow the tracking line on individual series: graph.getSerie("CA").allowTrackingLine( {} ); Does not need any prior options given to the graph instance. Can you implement an option in the visualizer. This way, when it breaks, I'll know soon enough :D

in jsGraph 1.11.3-11, graph.newSerie( name ), name has now to be unique. If the serie already exists, jsGraph will return the currently existing serie.

You should check your code that nothing will break before you upgrade the library

When we paste an image in the quill module on

https://www.lactame.com/visualizer/src/index.html?config=../testcase/config/default.json&viewURL=../testcase/data/quill/view.json&dataURL=../testcase/data/quill/data.json

We have the image that is pasted twice.

If we disable the module imageDrop it works correctly.

https://github.com/NPellet/visualizer/blob/7264cd6edd1ca0511a5999ca1220b47f4b48ac21/src/modules/types/edition/quill_editor/view.js#L88-L89

There is another plugin: https://www.npmjs.com/package/quill-image-drop-and-paste that could be tested

https://github.com/NPellet/visualizer/blob/d00e4f45ae8677eaf60e4125d1af434b29cc64e3/package.json#L85-L86

@stropitek could you have a look at this ?

Hi,

I tested getting Visualizer to run in a Node docker:

docker run -it --rm -p 8080:80 -v $(pwd):/nodeapp node bash
# in the docker: 
cd /nodeapp
npm install

This results in the following error. I tried with images node and node:16. Is this an obvious problem from my side?

root@96ac787d5393:/nodeapp# npm install
npm notice
npm notice New patch version of npm available! 8.1.2 -> 8.1.4
npm notice Changelog: https://github.com/npm/cli/releases/tag/v8.1.4
npm notice Run npm install -g [email protected] to update!
npm notice
npm ERR! code ERESOLVE
npm ERR! ERESOLVE unable to resolve dependency tree
npm ERR!
npm ERR! While resolving: [email protected]
npm ERR! Found: [email protected]
npm ERR! node_modules/grunt
npm ERR!   dev grunt@"^1.0.3" from the root project
npm ERR!
npm ERR! Could not resolve dependency:
npm ERR! peer grunt@"~0.4.1" from [email protected]
npm ERR! node_modules/grunt-rename
npm ERR!   dev grunt-rename@"^0.1.4" from the root project
npm ERR!
npm ERR! Fix the upstream dependency conflict, or retry
npm ERR! this command with --force, or --legacy-peer-deps
npm ERR! to accept an incorrect (and potentially broken) dependency resolution.
npm ERR!
npm ERR! See /root/.npm/eresolve-report.txt for a full report.

npm ERR! A complete log of this run can be found in:
npm ERR!     /root/.npm/_logs/2021-11-26T13_31_41_404Z-debug.log

In a twig form template when a variable is undefined we have a blank event but not an update event.

This has as consequence that the form disappear.

I would like that even if an input variable is undefined the rendering of the form still happens.

It can be test in the following testcase if you click on the button of the bottom executor module.

http://127.0.0.1:5501/src/index.html?config=../testcase/config/default.json&viewURL=../testcase/data/twig-form-light/view.json&dataURL=../testcase/data/twig-form-light/data.json

https://github.com/Lattice-Automation/seqviz

Possibility to have DNA sequences as input that are translated automatically

import { translateDNA } from "./utils/sequence";
let result = translateDNA("AAATTTCCCGGG");
console.log(result);

When loading a module you have an event that generate an action when the module is loaded. The problem is that you want to be sure that the action already exists otherwise it will not be executed obviously.

In order to be 'sure' that the action exists I add it in the general preferences. However I get random results. Apparently in some case the action out from the module is executed before the general preferences action has been loaded and I don't understand why.

The relate loading order is I think here:

https://github.com/NPellet/visualizer/blob/0369baee45b70071656a7b41771696cf75b4c520/src/src/main/entrypoint.js#L127-L148

Using a similar API as

function updatePreferences(moduleId, values)

It would be nice to also have the method

let values = getPreferences(moduleId);

The goal is really that we can do API.updatePreferences(4, API.getPreferences(4)); and nothing should change. I'm quite lost with alias and I don't know how easy it is to do.