It should enable the peaks picking option that allows users can select peaks manually. The current version doesn't have it. See the screenshot:

@CS76

{
version: <number>
spectra:[],
molecules:[],
// ... other properties 
}

what is missing in the data you save in the database is the version object which is important for the migration process that is done when importing the .nmrium object inside the NMRium and without it the NMRium went be able to display the data.

another thing worth mentioning is the migration functionality moved to nmr-load-save package which means we can use the migration separately if we need it to migrate the old data

When the auto-peak picking option is selected, we could highlight potential reference/solvent peak in the spectra

• Highlight the reference peak, possibly in a different colour.
• Suggest the correct shift value to avoid the need to look up tables
• Reference correction could be presented in one view showing a window suggesting the reference and its shift, asking the user for confirmation, correcting its shifts and the rest of the shift and deleting the solvent peak.

Can we disable drag and drop or file choose option on the nmrium via URL query parameter like the following
https://nmriumdev.nmrxiv.org?standalone=true

File import should work normally in other panels like molecules etc.

• Following the instructions in the README file, after docker running, (docker run \

  -it
  --rm
  -v ${PWD}:/app
  -v /app/node_modules
  -p 3001:3000
  -e CHOKIDAR_USEPOLLING=true
  nmrium-rw:dev)
  The app doesn't run on the mentioned port 3000, instead it gives a "Unable to connect" error.

• Additionally, the message shown in the terminal says that the port is 5173, which also doesn't work.

looks like .zip is being appended to the download link URL and this is going to break download links

Test it on nmrxiv dev site for more details please.

• List all nmrium versions and the corresponding data schema versions (in a table format and add it to the readme file in the nmrium-react-wrapper repository)
• nmrium-react-wrapper's nmrium version (dev/production)
• Compare the nmrium versions of the nmrxiv production nmrium instance and the latest nmrium release

How the workflow should be?

Let's say the user sends 2 files named analyse_1.dx and analyse_2.zip to the wrapper.
The user wants to save the preview image depending on which file she/he is working on.
She/he want to save the file name of the preview image as same as the file that she/he sent. For example, if she/he is working on analyse_2.zip, the preview image should be analyse_2.svg or 'analyse_2.png.

Questions

1. Do we have any option for this workflow?
2. If not, is it possible to implement it?

on dev: nmrium-react-wrapper when deployed should be accessible via nmrium.dev.nmrxiv.org
on prod: nmrium-react-wrapper when deployed should be accessible via nmrium.nmrxiv.org

Resources
https://medium.com/bb-tutorials-and-thoughts/deploying-react-with-nodejs-backend-on-gcp-gke-using-helm-e11f2480fff
https://koala42.com/create-a-react-app-in-kubernetes

While the two-way communication happens between the parent application and NMRium wrapper, event naming should be grouped via namespaces

nmr-wrapper:load:dataset
nmr-wrapper:load:spectra
nmr-wrapper:load:molecule
(loads spectra, load molecule data)

nmr-wrapper:export:image
nmr-wrapper:export:data
(export images, nmrium JSON, nmredata, string containing ranges, peaks, integrals etc)

nmr-wrapper:action:spectral-manipulation
nmr-wrapper:action:update-workspace

NMRium:

1. Choose about 5 of datasets with 1d and 2d NMR experimental raw data and known structure (nmrshiftdb)/ clean and noisy.
2. Explore ways to perform molecular assignments
3. Recreate/explore features from 2 Luc's demos
4. Compare the process with mnova (Johannes demo, Luc demo, Michael demo)
5. Reach to Johannes to offers help in docs
6. Record comparison

Sherlock:

1. Test with the same datasets.
2. Perform CASE steps. Check if expected structure among the predicted ones.
3. What Sherlock offers/ what blockers.

actionType used to provide info such as "INITIATE", "ADD_MOLECULE", "DELETE_MOLECULE" and this is no longer the case in the new version.

@CS76

we have to be careful when getting the data from onDataChange call-back to convert the data from the typed array to an array because without this step the NMRium is no longer able to load the data.

the implementation was not done at the side of NMRium for two reasons
1- concerns about the memory because the call-back is often called too much.
2- we need to listen to change and may want the typed array for another purpose

Do you think this has to be done in the wrapper or at your end?

• an abstract code sample for using the custom actions in the wrapper from nmrXiv.
• Add version key requirements in the data object passed to nmrium
• convert data from type array to an array

@NRayya @hamed-musallam please break this down to sub-tasks and assign b/w you both pls

We realized that the public nmrium-wrapper instance at Jena is running on data version 3, the development container already implements version 4.
As of now, we can't properly check what data version the nmrium wrapper uses besides "looking at the returned data structure". This doesn't seem to be a very robust way of doing it especially in the long run, so we suggest to add an API call to let applications know what data version to expect.

We would like to capture all the changes that our users might perform on the spectra. So, to enable this we need to propagate the onChange event from the nmrium react component to the parent via window message event and the parent application will then process/persist the data to the back end.

I found that when you are parsing the origin to check if it's in the allowed origins list, you are using your very own helper function to check if an IP is an IP address. However it seems to only work for legacy IP addresses, IPv6 seems not to be supported.

Can we get this?

(I also reference #59 as I think it might be helpful)

https://github.com/NFDI4Chem/nmrium-react-wrapper/wiki/4.-CI-CD

Schema to load Bruker Zip files from URL ?? @hamed-musallam

Here are the files, we are facing the issue with datasets 2,6, and 7
https://cloud.uni-jena.de/s/588LfmRnyTbiDT3

• Tools/scripts to offer conversion
• Examples and test cases to check if the new schemas break the conversion

Check if there are any whitelisted domains in the env variables and append them to the ones hardcoded. If none continue.

Once the data is published to the public, nmrXiv users would like to look into the assignments (browser) and other related assay parameters.

We need to offer a read-only view of the spectra using nmrium without the options or with the options disabled. The spectra viewer still needs to be interactive while the side panels just need to display data.

• Docs
• Install instructions
• Contributors
• Bug/Issue reporting

react-wrapper is reloading continuously when run locally ~ dev docker deployment

Move the host and port config to dedicated vite.config.js file

What we need:

• Transmit analysed data to other parties

Current status:

• Analysed data is saved as a downloaded file [see the video]
  https://user-images.githubusercontent.com/9006482/174767853-86d5a395-1bb8-4060-b8ba-dda522f2a7c1.mp4

Please check the new pre-release of NMRium read the integrals, ranges, and peaks, and display them correctly which was not right in the NMRium version 0.33 which was related to the new nmr-load-save package.

When using 1D jdf, everything works fine:

But with 2D jdf, NMRium can't read the file:

We want to load nmrium with different display options. Instead of sending all the preferences, it would be good to have this mapped on the wrapper side.

1. ?mode=viewer
   All the side panels need to be hidden, only the viewer is shown

2. ?mode=analysis
   The following panels need to be shown

?mode=analysis&panelWidth=100
Would be great if we can specify the width of the side panel in percentage

Two possible solutions we can adapt

1. Display the buttons only on the development instance. The production version should have this automatically hidden (subdomain check or via build process). Make sure this doesn't add up to the loading time of the application.

2. Totally hide this and register keyboard shortcuts to trigger these events. For example

Shft+Ctrl+1 => Test load custom event
Shft+ctrl+2 => Test load observable
Shft+ctrl+2 => Test load via URLS

pass preferences and workspace parameters with the URL to customize the NMRium

we encode preferences JSON data with a URL encode

{"toolBarButtons": {"import": true,"exportAs": true},"panels": {"multipleSpectraAnalysisPanel": { "hidden": true },"spectraPanel": { "hidden": true }}}

output

%7B%22toolBarButtons%22%3A%20%7B%22import%22%3A%20true%2C%22exportAs%22%3A%20true%7D%2C%22panels%22%3A%20%7B%22multipleSpectraAnalysisPanel%22%3A%20%7B%20%22hidden%22%3A%20true%20%7D%2C%22spectraPanel%22%3A%20%7B%20%22hidden%22%3A%20true%20%7D%7D%7D%0A

for example
https://nmriumdev.nmrxiv.org/?workspace=default&preferences=%7B%22toolBarButtons%22%3A%20%7B%22import%22%3A%20true%2C%22exportAs%22%3A%20true%7D%2C%22panels%22%3A%20%7B%22multipleSpectraAnalysisPanel%22%3A%20%7B%20%22hidden%22%3A%20true%20%7D%2C%22spectraPanel%22%3A%20%7B%20%22hidden%22%3A%20true%20%7D%7D%7D%0A

Currently, the preview image is svg format when calling exportSpectraViewerAsBlob. Do we have any option to get the png format or the other image formats?

When I save the data as *.nmrium and want to use it, it cannot be reloaded.
Could you check whether this file is correct or not?
I zipped this file for upload on github purpose
220204-5-H202.zip
Thank you!

Received:

Expected:

{ "data" : { "source" : [], "spectra" : [ { "selector": {} } ], "molecules" : [] }, "version": 4 }

@CS76

Current feature of NMRium wrapper

• Jcamp files (*.jdx files) are read default spectra data and meta data content.

Suggestion or discussion

• Can we support that transfer or read custom fields on jcamp files like peaks, multiplicity, and integrals?

• Task1
• Task2

@NRayya @hamed-musallam

• Backup existing observable implementation into a separate branch
• Tidy up development and use custom events going forward

We are planning to use this service i a dynamic environment where we can not foresee the origin URLs upfront. Would it be possible to allow skipping the origin checks altogether, if, for example, an environment variable is set? Obviously the service would then be publicly available, but in our case, we are fine with this or can handle it through origin checks in the network infrastructure.

I suggest something to the extend of replacing

with:

const skip_origin_check = "SKIP_ORIGIN_CHECK" in process.env && process.env.SKIP_ORIGIN_CHECK == 1
if (!skip_origin_check && !ALLOWED_ORIGINS.includes(parseOrigin(origin)) ) {
...

In NMRium test page, we can view the 2D data, but in NMRium wrapper we can't. See the video below:

Here is the file that was used in the video:
12.zip

Provide details of the new schema for event calls
Group the events

• Load
  URL
  NMRium JSON data
  File buffer
• Action requests details
  Image export as Blob
• Action response details
  Registering event listeners - message

I would suggest to optimize this code a bit and make use of the native URL interface.

It makes the parsing easier and probably more future-proof/safe (i.e. handles IPv6 addresses, which your code doesn't do as of now)

@hamed-musallam @NRayya