Write and Submit RFCs of nmrium file format

[tpoisseau]

Refs: #2523

Theses RFCs would describe each file format.

Today I consider we have 3 format (the last one is not finished yet) of nmrium files, I "invented" their mimetype (open to discussion):

• application/nmrium+json a text file with .nmrium extension. plain json compatible withSerializedNmriumState interface.
• application/nmrium+json+zip an application/nmrium+json in a zip file, also with .nmrium extension
• application/nmrium+zip an archive with .nmrium.zip containing
  • state.json file (plain json compatible withSerializedNmriumState interface, with no data but potential external sources reference)
  • .sdf files to be compatible with NMReData format (molecules) referencing files containing their related spectrum
  • index.json from ium archive format referencing sources (local in archive with ium:/ protocol and potentially external with https:// or http:// protocols)
  • data folder containing any files format supported by nmrium to extract nmr spectra (zip, nmredata, jcamp, bruker and so on)

I choose .nmrium.zip as extension to for better discoverability of our file format, It will be simplier for scientist to open a zip file a look at nmr spectra files included in it. But i'm open to discussion.

I wonder if we really need to do RFC and register our mimetypes at IANA or if mimetypes registery have some namespace or naming format available to define and use what we want with potential risk of conflicts without need to register them.

Refs: https://www.iana.org/assignments/media-types/media-types.xhtml

[tpoisseau]

@cheminfo/nmr

[lpatiny]

I choose .nmrium.zip as extension to for better discoverability of our file format, It will be simplier for scientist to open a zip file a look at nmr spectra files included in it. But i'm open to discussion.

I like this idea. I was always hesitating between .zip and .nmrium.

For non official mimetype seems x- is used.

There is a wikipedia page that we could edit with chemical format. But even them are not official: https://en.wikipedia.org/wiki/Chemical_file_format. In this page the JCAMP-DX is already defined (chemical/x-jcamp-dx).

Based on this page I would go for:

• chemical/x-nmrium+json
• chemical/x-nmrium+json+zip
• chemical/x-nmrium+zip

Will those 2 formats survive ?

• application/nmrium+json
• application/nmrium+json+zip

I think when loading those 2 formats they will be migrated to the new format (application/nmrium+zip). Even if we 'save as...' without data I think it could be a zip file with state.json as only file.

Defining the mimetype / extension should allow to open the PWA based on extension https://developer.mozilla.org/en-US/docs/Web/Progressive_web_apps/Manifest/Reference/file_handlers.

[tpoisseau]

mimetype exist only in this issue for the moment (and recent tsdoc in my actual PR, simple to change).

See: https://sqlite.org/appfileformat.html

For me, our nmrium file format is a "Wrapped Pile-of-Files Format". So intuitively i would go for application/x- prefix hover chemical/x- but I'm open to chemical/x-.

So let's say we validate chemical/x-nmrium+json, chemical/x-nmrium+json+zip, chemical/x-nmrium+zip.

About +json and +json+zip variants. For me the plan is:

1. Purpose +zip variant with experimental indication, and stabilize it. (Only the serialization is ready in my PR yet).
2. Once it is considered stable, deprecate +json and +json+zip variants. save and save as default to +zip.
3. Remove the possibility to export into +json and +json+zip variants but keep the ability to read them for backward compatibility.

NB: a little interrogation about +json+zip format. it's due to compressed option. why did not we use standard .gz extension and compress the file with gzip, instead producing a zip archive for a single file (and keeping the same .nmrium extension for both format) ?

[tpoisseau]

So let's say we validate chemical/x-nmrium+json, chemical/x-nmrium+json+zip, chemical/x-nmrium+zip.

Done, application/ mimetype prefix for nmrium should not appear anymore in code base, nor in spec draft.

[lpatiny]

Ok thanks. Once the new version is in production I will edit the wikipedia page.