mrc-2476: Upgrade ajv to version 8.5.0 and include draft-04 extension

[r-ash]

See https://ajv.js.org/json-schema.html#draft-04

• Upgrade ajv to 8.5.0
• Include draft-04 schema extension
• Include ajv-formats plugin
• Add arg strict to json_validator and json_validate FALSE by default which allows permissive handling of schema validation see https://ajv.js.org/strict-mode.html
• If running with schema > draft-04 then fallback to using ajv and print message to user
• Add dataPath property to verbose errors, for backwards compatibility as this has been renamed to instancePath in ajv version 8+

Checked this is working with biocompute, and with hintr. Checked this is working with dependencies using revdepcheck::revdep_check() too - failing on TKCat

Issues encountered (which I think I have fixed)

• TKCat uses new 2019-09 schema - "$schema": "https://json-schema.org/draft/2019-09/schema", https://github.com/patzaw/TKCat/blob/master/inst/Collections/Collection-Schema.json#L2 . Ajv supports this see https://ajv.js.org/v6-to-v8-migration.html - tried to work around that by updating the version parsing and making 2019-09 and 2020-12 available
• dccvalidator failing as it uses dataPath returned in table of errors which has been renamed in instancePath in updated ajv, see https://github.com/Sage-Bionetworks/dccvalidator/blob/5dc13f7f77d6444226e3031c1210190937a78682/R/check-schema-json.R#L58 - tried to work around this by duping dataPath to instancePath
• tableschema.r fails if run with ajv because ajv returns 4 errors where imjv returns 1 (we can work around this if we continue to use imjv for draft-04 by default`
• biocompute uses references which we don't want to fail on e.g. https://github.com/sbg/biocompute/blob/master/inst/schemas/1.3.0-alpha/biocomputeobject.json#L86

Remaining issue

• TKCat uses "$schema": {"enum": ["TKCat_collections_1.0"]}, which throws

Unknown meta schema version 'TKCat_collections_1.0'
E> --- failed re-building ‘TKCat-Collections.Rmd

With cran version they are validating against imjv. But with updated version currently on master this won't work as it tries to parse the version of the schema so it errors early if not using draft-04. This didn't error previously so I assume validated permissively. Now updated to support 2019-09 this is failing validation on ajv. I don't really know what this is - some kind of metaschema? Not sure if "$schema": {"enum": ["TKCat_collections_1.0"]} is ever valid?

[richfitz]

Nice, this is fantastic. A few minor changes below, most important is to check that we didn't break any of the other packages (if we did we'll need to leave imjv as the default, perhaps unless draft >= 4 is detected)

[richfitz]

If we make this change we might break other packages, can you check please?

https://cran.r-project.org/web/packages/jsonvalidate/index.html - see devtools::revdep to automate

[richfitz]

While we're here, could you rename tmp to something better (validator, perhaps?)

[richfitz]

Aha, is that how you do this?

[richfitz]

What happens if we try and use imjv with a meta schema version of draft-6/7? Still throws an error? We should probably document that. Also the docstring for engine needs updating to reflect the new default

[r-ash]

It still throws an error yeah - this referenced issue from the code mafintosh/is-my-json-valid#160 still a problem