Write a prototype script to generate a method section from the output of the app

[Remi-Gau]

What am I supposed to do with this bunch of JSON files?

The obviously missing piece from this project is part that allows converting the ouput of the app into a human readable method section any researcher can copy into their article.

The goal of this sub-project is to create some prototype scripts to:

• extract the relevant content from the JSON files one can download from the web app
• read some templates that contain the boilerplate method section with some "blanks" for the part to be filled in.
• fill in the blanks
• output the results in a file in a format that is easy to convert to something else (markdown?)

We are not starting from scratch !

We already have a "library of boilerplates" method sections we could use for prototyping: see HERE.

Also, some softwares from the BIDS ecosystem also do some basic things like that for some BIDS data set:

• pybids report (also see this pull request)
• bids-matlab and see this pull request
• fMRIprep
• MNE
• This prototype repo for BIDS MEG started by Guiomar Niso

To restrict the scope of this sub-task let's start by focusing on items in eCobidas that overlap with those of the BIDS world and so mostly for the "data acquisition" section of the guidelines.

This could also help create template methods that can later be reused by the BIDS eco-system more easily

Some low hanging fruits:

• create a template section for:
  • EEG and MEG that can also be reused
  • physio part of a BIDS dataset
  • events part of a BIDS dataset

Contraints to keep in mind

The "format" chosen for the templates should be sufficiently language agnostic to be reusable fairly easly by python, javascript, matlab...