XRD Hackathon: using a `nexus` subsection

[budschi]

Since the nexus section resolved into data recently, we have to use now a subsection which we could call nexus instead of the nexus section we had beofore. Otherwise there will be an overwriting conflict.

@sanbrock @markus1978

[RubelMozumder]

@budschi FYI: The PR #116 has not been yet merged into the main branch.

The creation of a nexus sub-section in the EntryArchive or in EntryArchive/data is not an issue. Currently, in PR #116 data comes from the Nexus file using the hdf5 reference recipe. There are no nexus subsections anywhere. I tested the XRD measurement plugin there are no issues. @ka-sarthak would you please confirm it?

[budschi]

Sandor and I discussed the following today:

• workflow NOMAD Measurement Plugin = NMP
  3rdparty = follwing an App Def, may also contain alien information (not in NMP)
  • 1. myxrd.xrdml --> NMP --> ELNXRD view of myxrd.archive.json
  • 2. myxrd.xrdml --> NMP+App. Def. --> ELNXRD view of myxrd.archive.json + myxrd.nxs (ELN has references to nxs) missing: "Nexus" Section --> to be replaced by a Reference to a Nexus entry
  • 3. 3rdpartyxrd.nxs --> NMP + App.Def. --> 3rdpartyxrd.nxs (same as the referenced on in 2.) missing: NMP would need to create an ELN with 3rdpartyxrd.archive.json and establish a reference
• questions, comments to workflow:
  • does 1. + 2. result in the same "ELN" in NOMAD?
  • missing in 2:
  • does 3. exist? --> should be there!

• Implementation workflow

  • scenario:

    1. custom plugin for XRD --> branch of NM with this method
    2. NOMAD Measurement plugin with structure according to [nomad-plugin-template](https://github.com/FAIRmat-NFDI/nomad-plugin-template)
    3. Nxs app def available --> additional support for Nexus standard

  • what consequences does 3 have on implementation? Need for pynx tool? etc?

    • requires use of pynxtools --> generates *.nxs
    • file readers in pynxtool:
      • may exist --> nothing todo
      • may not exist as we want (missing custom ELNXRD fields): extend reader to also populate extra fields in Nexus file
      • no reader for input format: build new reader from an example in pynxtool --> pynxtool plugin in github
      • when you write pynxtool reader you can reuse reader functionalities from elsewhere by importing!
    • once *.nxs exists:
      • change NM parser to support references --> ideally to nexus entry not a nxs/h5 file

  • Pynxtool plugin:

• Next milestone
  • making relationships between the concepts making the references in the ideal way
  • how reuse NeXus description iin the backgrond and not in the ELn view