Using SQL Databases

SQL Alchemy is a SQL framework for python. It has a core layer, and an ORM layer.

See:

The SQLStore class provides a convenient wrapper around these generators for working with SQL Data

SQLStore

class linkml.utils.sqlutils.SQLStore(schema: Optional[Union[str, linkml_runtime.linkml_model.meta.SchemaDefinition]] = None, schemaview: Optional[linkml_runtime.utils.schemaview.SchemaView] = None, engine: Optional[sqlalchemy.engine.base.Engine] = None, database_path: Optional[str] = None, module: Optional[module] = None, native_module: Optional[module] = None, include_schema_in_database: Optional[bool] = None)[source]

A wrapper for a SQLLite database.

This provides two core operations for storing and retrieving data

The wrapper transparently will take care of:

  • mapping your LinkML schema into SQL Tables

  • creating a SQL Alchemy ORM layer

  • mapping your data/objects in any LinkML compliant data format (json. yaml, rdf) into ORM objects

compile() → module[source]

Compile SQLAlchemy object model

Uses Declarative by default.

Note that the SQLA model is different from the native dataclass model

Returns

compiled module

compile_native() → module[source]

Compile native python object model

Returns

compiled module

db_exists(create=True, force=False) → str[source]

check if database exists, optionally create if not present

Parameters

  • create – create if does not exist

  • force – recreate database, destroying any content if previously present

Returns

path

dump(element: linkml_runtime.utils.yamlutils.YAMLRoot, append=True) → None[source]

Store an element in the database

Parameters

  • element –

  • append –

Returns

from_sqla(obj: Any) → Optional[Union[linkml_runtime.utils.yamlutils.YAMLRoot, List[linkml_runtime.utils.yamlutils.YAMLRoot]]][source]

Translate from SQLAlchemy declarative module to native LinkML

Parameters

obj – sqla object

Returns

native dataclass object

load(target_class: Optional[Union[str, Type[linkml_runtime.utils.yamlutils.YAMLRoot]]] = None) → linkml_runtime.utils.yamlutils.YAMLRoot[source]

Loads a LinkML object from the wrapped SQLite database

Parameters

target_class –

Returns

to_sqla(obj: Union[linkml_runtime.utils.yamlutils.YAMLRoot, list]) → Any[source]

Translate native LinkML object to SQLAlchemy declarative module

Parameters

obj –

Returns

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