update example data to napa -style identifiers

[aclum]

After re-iding is complete and the materialized pattern version of the schema is enforced some of the example data will fail validation because there are legacy style identifiers. We can & should fix some of this in advance.

[aclum]

@turbomam took care of this several months ago.

[aclum]

This is fixed for IDs but not ID mentions.

[aclum]

@turbomam not quite sure what to do here. These are hard to find out with structured_pattern enforced for IDs and ID mentions. Some of this is fixed in Berkeley.

[turbomam]

Yeah, this is one of those things where the progress made in nmdc-schema and berkeley-schema-fy24 isn't totally clear

I'll

• try to make detection of pattern constraints in the schema clearer
• provide tools for checking the examples against the various forms of the schema
  • src/schema/*.yaml
  • nmdc_schema/nmdc_materialized_patterns.yaml (and project/nmdc_materialized_patterns.yaml)
  • nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml
  • nmdc_schema/nmdc_schema_merged.yaml (and project/nmdc_schema_merged.yaml)
  • project/nmdc_schema_generated.yaml

[aclum]

This PR addressed constraints on ID mentions which required updating all the example data to make it match. @bmeluch is separately going to review the invalid data to make sure tests fail or one and one one reason.

[aclum]

Assigning to @bmeluch so she can update the invalid example data. I fixed a lot of this in Berkeley but not in nmdc-schema.

[bmeluch]

Being addressed in Berkeley as part of https://github.com/microbiomedata/berkeley-schema-fy24/pull/220