SQLite conversion ERROR:root:UNKNOWN range base: None for gold_sample_identifiers = external identifier

[turbomam]

poetry run linkml-sqldb dump \
            --db data_7.db \
            --target-class Database \
            --schema src/schema/nmdc.yaml data_7.json

[turbomam]

As in #500, changing external_database_identifiers's range from external identifier to uriorcurie eliminates this non-terminating "error"

[turbomam]

But the change mentioned above does not solve the terminating errors

• sqlalchemy.exc.AmbiguousForeignKeysError: Can't determine join between 'Activity' and 'Agent'; tables have more than one foreign key constraint relationship between them. Please specify the 'onclause' of this join explicitly.
• sqlalchemy.exc.AmbiguousForeignKeysError: Could not determine join condition between parent/child tables on relationship Activity.was_associated_with - there are multiple foreign key paths linking the tables. Specify the 'foreign_keys' argument, providing a list of those columns which should be counted as containing a foreign key reference to the parent table.

[turbomam]

https://microbiomedata.github.io/nmdc-schema/was_informed_by/

src/schema/prov.yaml says

classes:

  Activity:
    description: "a provence-generating activity"
    slots:
      - id
      - name
      - started_at_time
      - ended_at_time
      - was_informed_by
      - was_associated_with
      - used
    mappings:
      - prov:Activity

and

  was_associated_with:
    range: Agent
    mappings:
      - prov:wasAssociatedWith

but src/schema/workflow_execution_activity.yaml says

classes:
  WorkflowExecutionActivity:
    aliases:
      - analysis
    comments:
      - Each instance of this (and all other) activities is  a distinct run with start and stop times, potentially with different inputs and outputs
    is_a: Activity
    in_subset:
      - workflow subset
    description: >-
      Represents an instance of an execution of a particular workflow
    alt_descriptions:
      embl.ena: >-
        An analysis contains secondary analysis results derived from sequence reads (e.g. a genome assembly)
    slots:
      - raw_type
      - execution_resource
      - git_url
      - has_input
      - has_output
      - part_of
      - type # custom slot that specifies object type
    slot_usage:
      was_associated_with:
        required: false
        description: >-
          the agent/entity associated with the generation of the file
        range: WorkflowExecutionActivity
        inlined: false # allow for strings of IDs

[turbomam]

• Activity
  • WorkflowExecutionActivity
  • MetagenomeAssembly
  • MetatranscriptomeAssembly
  • MetagenomeAnnotationActivity
  • MetatranscriptomeAnnotationActivity
  • MetatranscriptomeActivity
  • MagsAnalysisActivity
  • ReadQcAnalysisActivity
  • ReadBasedTaxonomyAnalysisActivity
  • MetabolomicsAnalysisActivity
  • MetaproteomicsAnalysisActivity
  • NomAnalysisActivity