MongoDB data repair and schema loosening. DON'T FORGET TO RESOTRE THE `id`'s `strucutred_patterns` like 'syntax: "{id_nmdc_prefix}:'... about nmdc-schema

[turbomam]

Added the following targets to project.Makefile

• local/mongodb-collection-report.txt
• local/selected_mongodb_contents.json
• dump-validate-report-convert-mongodb
• mongodb-cleanup
• local/selected_mongodb_contents_jsonschema_check.txt
• linkml-validate-mongodb
• local/selected_mongodb_contents.yaml
• local/selected_mongodb_contents.ttl

[turbomam]

Looser alternative identifier pattern in src/schema/basic_slots.yaml

--- a/src/schema/basic_slots.yaml
+++ b/src/schema/basic_slots.yaml
@@ -98,7 +98,7 @@ slots:
multivalued: true
description: >-
A list of alternative identifiers for the entity.

old: pattern: '^[a-zA-Z_][a-zA-Z0-9_]:[a-zA-Z_][a-zA-Z0-9_]$'
new: pattern: '^[a-zA-Z0-9][a-zA-Z0-9_.]+:[a-zA-Z0-9_][a-zA-Z0-9_-/.]*$'

[turbomam]

Removed id's structured_patterns on several classes in src/schema/core.yaml. For lenience with legacy ids in MongoDB. Should be reintroduced for production/main/release.

Added a pattern for id in PlannedProcess

slot_usage:
   id:
     pattern: '^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.]*$'

[turbomam]

Loosened patterns in src/schema/external_identifiers.yaml

old: pattern: '^[a-zA-Z0-9][a-zA-Z0-9_.]+:[a-zA-Z0-9_][a-zA-Z0-9_/.]*$'

new: pattern: '^[a-zA-Z0-9][a-zA-Z0-9_.]+:[a-zA-Z0-9_][a-zA-Z0-9_-/.]*$'

renamed external identifier type to external_identifier

[turbomam]

Removed id's structured_patterns on several classes in src/schema/nmdc.yaml. For lenience with legacy ids in MongoDB. Should be reintroduced for production/main/release.

Added dubious emsl prefix with http://example.org/emsl_in_mongodb/ expansion because it appears in MongoDB records.

• which records in which collections?

[turbomam]

Removed id's structured_patterns on several classes in src/schema/prov.yaml. For lenience with legacy ids in MongoDB. Should be reintroduced for production/main/release.

changed range of started_at_time and ended_at_time from datetime to (implicit?) string.

[turbomam]

Removed id's structured_patterns on several classes in src/schema/sample_prep.yaml. For lenience with legacy ids in MongoDB. Should be reintroduced for production/main/release.

[turbomam]

Removed id's structured_patterns on several classes in src/schema/workflow_execution_activity.yaml. For lenience with legacy ids in MongoDB. Should be reintroduced for production/main/release.

made was_informed_by optional in class ???

• revert that?

gave used in classed MetabolomicsAnalysisActivity, MetaproteomicsAnalysisActivity and NomAnalysisActivity an implicit string range, instead of Instrument. This current usage ofused is more in the spirit of instrument_name, for which a new enum has been created but not applied.

[turbomam]

to find the structured_patterns of ids that need to be restores, search for

syntax: "{id_nmdc_prefix}:

[aclum]

Is this complete?