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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • OntologyLoaderController(mode=...) kwarg accepting 'meticulous' (default) or 'fast-initial'.
    • meticulous preserves 0.2.x behavior exactly: pure linkml-store, per-item upsert, force-refresh of the pystow cache, TSV reports written to report_directory.
    • fast-initial is the new maximum-throughput first-time-install path: raw pymongo insert_many(ordered=False), no pre-read, no upsert, no report tracking, no TSV writes. Reuses the pystow cache if present.
  • OntologyLoaderController(closure=...) kwarg accepting a string or list. Values: combined (default), isa, partof, all (exclusive shorthand for combined+isa+partof), none (exclusive — emit no ancestry closure).
  • OntologyLoaderController(report_directory=...) kwarg — renamed from output_directory.
  • OntologyLoaderController(source_ontology=...) now accepts a list of strings as well as a single string. Multiple ontologies are processed sequentially in the given order; failure on one halts the run.
  • New CLI surface — four flags total: --source-ontology (repeatable, required), --report-directory, --mode, --closure (repeatable).
  • MongoDBLoader.insert_ontology_data_fast_initial(...) — the raw-pymongo write method used by mode='fast-initial'.
  • OntologyProcessor(force_refresh=...) constructor kwarg — True (default) preserves 0.2.x cache-wiping behavior; False reuses the cached pystow artifact when present.

Changed

  • OntologyProcessor.get_relations_closure() signature: predicates= removed in favor of closure= (string or list of strings). The old hardcoded ancestry-relation name (entailed_isa_partof_closure) is now selected per-closure: entailed_isa_partof_closure, entailed_isa_closure, or entailed_partof_closure.
  • CLI no longer takes --generate-reports. Equivalents under the new design:
    • Old --generate-reports true (the implicit default) → new --mode meticulous (the default).
    • Old --generate-reports false → new --mode fast-initial.

Deprecated

  • OntologyLoaderController(output_directory=...) — use report_directory= instead. The old kwarg is an alias and emits DeprecationWarning. Passing both raises ValueError.
  • OntologyLoaderController(generate_reports=True) — no-op with DeprecationWarning. (True was always the default.)
  • OntologyLoaderController(generate_reports=False) — maps to mode='fast-initial' with DeprecationWarning. If mode was also passed and isn't 'meticulous', raises ValueError.

Removed

  • (nothing removed in this release — all 0.2.x kwargs continue to work as deprecated aliases. Removal slated for the next major release after downstream callers — notably the nmdc-runtime Dagster job — migrate.)

Migration

The exact 0.2.x call site in nmdc-runtime's Dagster op (nmdc_runtime/site/ops.py, load_ontology) — OntologyLoaderController(source_ontology=str, output_directory=str, generate_reports=True, mongo_client=..., db_name=...) — runs unchanged under this release. Two DeprecationWarning lines appear in the Dagster logs as a nudge to update.

To migrate when convenient:

# 0.2.x
OntologyLoaderController(
    source_ontology="envo",
    output_directory="/tmp/ontology_reports",
    generate_reports=True,
    mongo_client=client,
    db_name="nmdc",
)

# 0.3.0+
OntologyLoaderController(
    source_ontology="envo",        # or ["envo", "po", "uberon"]
    report_directory="/tmp/ontology_reports",
    mode="meticulous",             # default; or "fast-initial"
    closure="combined",            # default; or "isa", "partof", "all", "none", or a list
    mongo_client=client,
    db_name="nmdc",
)