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feat: enable label validation by default #8

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Merged
dragon-ai-agent merged 1 commit into from
Dec 18, 2025
Merged

feat: enable label validation by default #8

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -516,7 +516,7 @@ See the [examples/](examples/) directory for complete examples:
```yaml
"linkml_term_validator.plugins.BindingValidationPlugin":
oak_adapter_string: "sqlite:obo:" # OAK adapter (default: sqlite:obo:)
validate_labels: true # Check labels match ontology (default: false)
validate_labels: true # Check labels match ontology (default: true)
cache_labels: true # Enable label caching (default: true)
cache_dir: cache # Cache directory (default: cache)
oak_config_path: oak_config.yaml # Optional: custom OAK config
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2 changes: 1 addition & 1 deletion docs/binding-validation.md
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Expand Up @@ -357,7 +357,7 @@ for result in report.results:
|-----------|------|---------|-------------|
| `oak_adapter_string` | `str` | `"sqlite:obo:"` | Default OAK adapter |
| `oak_config_path` | `str \| None` | `None` | Path to OAK config file |
| `validate_labels` | `bool` | `False` | Also validate labels |
| `validate_labels` | `bool` | `True` | Also validate labels |
| `strict` | `bool` | `True` | Fail when term IDs not found in configured ontologies |
| `cache_labels` | `bool` | `True` | Enable file-based caching |
| `cache_dir` | `str` | `"cache"` | Cache directory |
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4 changes: 2 additions & 2 deletions docs/plugin-reference.md
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Expand Up @@ -289,7 +289,7 @@ from linkml_term_validator.plugins import BindingValidationPlugin
plugin = BindingValidationPlugin(
oak_adapter_string="sqlite:obo:",
oak_config_path=None,
validate_labels=False,
validate_labels=True,
cache_labels=True,
cache_dir="cache",
)
Expand All @@ -301,7 +301,7 @@ plugin = BindingValidationPlugin(
|-----------|------|---------|-------------|
| `oak_adapter_string` | `str` | `"sqlite:obo:"` | Default OAK adapter string for ontology access |
| `oak_config_path` | `str \| None` | `None` | Path to `oak_config.yaml` for per-prefix adapter configuration |
| `validate_labels` | `bool` | `False` | If `True`, also validate that labels match ontology canonical labels |
| `validate_labels` | `bool` | `True` | If `True` (default), also validate that labels match ontology canonical labels |
| `cache_labels` | `bool` | `True` | Enable file-based caching of ontology labels |
| `cache_dir` | `str` | `"cache"` | Directory for cache files |

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6 changes: 3 additions & 3 deletions src/linkml_term_validator/cli.py
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Expand Up @@ -171,9 +171,9 @@ def validate_data(
bool,
typer.Option(
"--labels/--no-labels",
help="Validate labels match ontology",
help="Validate labels match ontology (default: enabled)",
),
] = False,
] = True,
lenient: Annotated[
bool,
typer.Option(
Expand Down Expand Up @@ -406,7 +406,7 @@ def validate_all(
target_class=None,
validate_bindings=True,
validate_dynamic_enums=True,
validate_labels=False,
validate_labels=True,
lenient=lenient,
adapter=adapter,
cache_dir=cache_dir,
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6 changes: 3 additions & 3 deletions src/linkml_term_validator/plugins/binding_plugin.py
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Expand Up @@ -13,7 +13,7 @@
>>> plugin.strict
True
>>> plugin.validate_labels
False
True
>>> plugin.expanded_enums
{}

Expand Down Expand Up @@ -92,7 +92,7 @@ class BindingValidationPlugin(BaseOntologyPlugin):
def __init__(
self,
oak_adapter_string: str = "sqlite:obo:",
validate_labels: bool = False,
validate_labels: bool = True,
strict: bool = True,
cache_labels: bool = True,
cache_dir: Path | str = Path("cache"),
Expand All @@ -103,7 +103,7 @@ def __init__(

Args:
oak_adapter_string: Default OAK adapter string (e.g., "sqlite:obo:")
validate_labels: If True, also validate that labels match ontology
validate_labels: If True (default), also validate that labels match ontology
strict: If True (default), fail when term IDs are not found in configured ontologies
cache_labels: Whether to cache ontology labels to disk
cache_dir: Directory for label cache files
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