deno (and legacy): Define and validate config file against target schema

[yarikoptic]

Could take all the error codes from the schema etc. But more so -- validate overall structure!

ATM neither legacy nor deno validators seems to care about config file being misspecified, e.g. with

❯ cat .bids-validator-config--totallywrong.json
["mess"]

there is neither complaint from legacy validator

❯ podman run -it --rm -v "${PWD}:${PWD}:ro" -w "${PWD}" bids/validator --config $PWD/.bids-validator-config--totallywrong.json asl001
[email protected]
	1: [ERR] This file is too small to contain the minimal NIfTI header. (code: 36 - NIFTI_TOO_SMALL)
		./sub-Sub103/anat/sub-Sub103_T1w.nii.gz
		./sub-Sub103/perf/sub-Sub103_asl.nii.gz

	Please visit https://neurostars.org/search?q=NIFTI_TOO_SMALL for existing conversations about this issue.

        Summary:                Available Tasks:        Available Modalities: 
        8 Files, 94.63KB                                MRI                   
        1 - Subject                                                           
        1 - Session                                                           


	If you have any questions, please post on https://neurostars.org/tags/bids.
 

nor from deno one

❯ deno run --allow-read --allow-env --reload -A https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js --config .bids-validator-config--totallywrong.json asl001
	[WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.
		GeneratedBy
		/dataset_description.json

		SourceDatasets
		/dataset_description.json

	Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.

	[WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.
		DeviceSerialNumber
		/sub-Sub103/anat/sub-Sub103_T1w.nii.gz
		/sub-Sub103/perf/sub-Sub103_asl.nii.gz

....

edit 1: relates to the fact that schema seems has changed for deno - I found

bids-validator/bids-validator/src/README.md

Line 21 in d1a5bf9

### Configuration file

and legacy syntax doesn't work.

Resting on the fact that there is no validation it seems to be possible to "encode" both old legacy and new deno validation configs

here is an example

❯ cp .bids-validator-config--conflicting2.json .bids-validator-config--conflicting2-deno.json
❯ cat .bids-validator-config--conflicting2-deno.json
{
  "ignore": [
     "NIFTI_TOO_SMALL",
     "SIDECAR_KEY_RECOMMENDED",
     "NIFTI_HEADER_UNREADABLE",
     "TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT",
     "JSON_KEY_RECOMMENDED"
    ]
}
❯ sed -i -e 's|\("[A-Z][^"]*"\)|\1, { "code": \1 }|g' .bids-validator-config--conflicting2-deno.json
❯ cat .bids-validator-config--conflicting2-deno.json
{
  "ignore": [
     "NIFTI_TOO_SMALL", { "code": "NIFTI_TOO_SMALL" },
     "SIDECAR_KEY_RECOMMENDED", { "code": "SIDECAR_KEY_RECOMMENDED" },
     "NIFTI_HEADER_UNREADABLE", { "code": "NIFTI_HEADER_UNREADABLE" },
     "TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT", { "code": "TOTAL_ACQUIRED_VOLUMES_NOT_CONSISTENT" },
     "JSON_KEY_RECOMMENDED", { "code": "JSON_KEY_RECOMMENDED" }
    ]
}

# old validator works
❯ podman run -it --rm -v "${PWD}:${PWD}:ro" -w "${PWD}" bids/validator --config $PWD/.bids-validator-config--conflicting2-deno.json asl001
[email protected]
This dataset appears to be BIDS compatible.
        Summary:                Available Tasks:        Available Modalities: 
        8 Files, 94.63KB                                MRI                   
        1 - Subject                                                           
        1 - Session                                                           


	If you have any questions, please post on https://neurostars.org/tags/bids.

# and deno too

❯ deno run --allow-read --allow-env --reload -A https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js --config .bids-validator-config--conflicting2-deno.json asl001

          Summary:                         Available Tasks:        Available Modalities:
          8 Files, 96.9 kB                                         MRI                  
          1 - Subjects 1 - Sessions                                                     

	If you have any questions, please post on https://neurostars.org/tags/bids.