Caching

The validator uses multi-level caching to speed up repeated validations and avoid redundant ontology queries.

In-Memory Cache

During a single validation run, ontology labels are cached in memory. If multiple permissible values reference the same term, it's only looked up once.

This cache exists only for the duration of the validation process and is discarded afterward.

File-Based Cache

Labels are persisted to CSV files in the cache directory (default: ./cache):

cache/
├── go/
│   └── terms.csv      # GO term labels
├── chebi/
│   └── terms.csv      # CHEBI term labels
└── uberon/
    └── terms.csv      # UBERON term labels

Cache File Format

Cache files use a simple CSV format:

curie,label,retrieved_at
GO:0008150,biological_process,2025-11-15T10:30:00
GO:0007049,cell cycle,2025-11-15T10:30:01

Cache Behavior

First run: Queries ontology databases, saves results to cache
Subsequent runs: Loads from cache files (very fast, no network/database access)
Cache location: Configurable via --cache-dir flag
Disable caching: Use --no-cache flag

Configuration

CLI

# Use custom cache directory
linkml-term-validator validate-schema --cache-dir /path/to/cache schema.yaml

# Disable caching
linkml-term-validator validate-schema --no-cache schema.yaml

Python API

from linkml_term_validator.plugins import DynamicEnumPlugin

plugin = DynamicEnumPlugin(
    cache_dir="/path/to/cache",
    cache_labels=True  # Enable/disable file-based caching
)

linkml-validate Configuration

plugins:
  "linkml_term_validator.plugins.DynamicEnumPlugin":
    oak_adapter_string: "sqlite:obo:"
    cache_labels: true
    cache_dir: cache

When to Clear Cache

You might want to clear the cache if:

Ontology databases have been updated and you need the latest labels
You suspect stale or incorrect labels in cached data
You're testing validation behavior and want to force fresh lookups

# Clear cache for specific ontology
rm -rf cache/go/

# Clear entire cache
rm -rf cache/

Performance Benefits

Caching provides significant performance improvements:

First validation: May take several seconds per ontology (database queries)
Cached validations: Typically < 100ms (CSV file reads)
No network dependency: Cached validations work offline

Cache Safety

The cache is read-only during validation and only contains: - CURIEs (ontology identifiers) - Canonical labels - Timestamps

Cached data cannot affect validation logic, only speed up lookups.