Update structured_pattern in basic_classes

[kheal]

Partially addresses: microbiomedata#1988 .

Checking that the use of the structured_pattern slot is appropriately defined on all classes that were refactored. This PR will also update all example data to comply.

When referencing a WorkflowExecution subclass it should be:

        structured_pattern:
          syntax: "{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}{id_version}$"

Otherwise it should be:

        structured_pattern:
          syntax: "{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$"

[kheal]

@aclum and @turbomam . I've updated the id slot usage to better reflect the expected patterns and require the {id_version} for the WorkflowExecution subclasses. Tests are failing because I have not updated references of these classes in the exmaple data - there are 404 instances I'd need to fix (see below for summary). I could do that, but I'm worried about merge conflicts.

I'd rather we back merge nmcd_schema into berkeley_schema_fy24 first. Then I will update this branch and PR and fix the examples. Thoughts?

[kheal]

This should not have version, will fix.

[aclum]

@turbomam and I have talked about making this class abstract. Let's finalize the plan, if its abstract we can remove the structured_pattern.syntax.

[kheal]

I'd like to be part of those conversations. I don't quite see how we can make the CalibrationInformation abstract unless we subclass it, but maybe I'm missing something. I expect to instantiate instances of CalibrationInformation with the metabolomics metadata generation.

[aclum]

Sorry, that was not a good place to leave that comment, I was referring about making WorkflowExecution abstract, not CalibrationInformation. This class seems like its not in the correct yaml, everything else in this yaml is for classes downstream of DataGeneration. Do you know the history on why this class is in this file and not nmdc.yaml?

[kheal]

Oh yeah.....long story but the nmdc.yaml sources the workflow_execution.yaml but not vice versa. The CalibrationInformation is the range of the has_calibration slot which is on some of the WorkflowExecutions (until we merge in Berkeley and apply some ingestions). Once that has_calibration slot and range is fixed, we can move this class and associated slot definition to the nmdc.yaml.

WorkflowExecution is already abstract on berkeley fork, which makes total sense to me.

[aclum]

@mbthornton-lbl @scanon do we want versioning on the workflow chain records?

[aclum]

Agree it makes sense to do this after a backmerge.