SQLStore#

class linkml.utils.sqlutils.SQLStore(schema: Optional[Union[str, SchemaDefinition]] = None, schemaview: Optional[SchemaView] = None, engine: Optional[Engine] = None, database_path: Optional[str] = None, use_memory: bool = False, module: Optional[module] = None, native_module: Optional[module] = None, include_schema_in_database: Optional[bool] = None)[source]#

A wrapper for a SQLite database.

This provides two core operations for storing and retrieving data

dump()
load()

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) → Optional[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: YAMLRoot, append=True) → None[source]#

Store an element in the database

Parameters:

element –
append –

Returns:

from_sqla(obj: Any) → Optional[Union[YAMLRoot, List[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[YAMLRoot]]] = None) → YAMLRoot[source]#

Loads a LinkML object from the wrapped SQLite database

Parameters:: target_class –
Returns:

to_sqla(obj: Union[YAMLRoot, list]) → Any[source]#

Translate native LinkML object to SQLAlchemy declarative module

Parameters:: obj –
Returns:

use_memory: bool = False#: https://docs.sqlalchemy.org/en/20/dialects/sqlite.html#using-a-memory-database-in-multiple-threads

Command Line#

linkml-sqldb#

Run the LinkML SQL CLI.

linkml-sqldb [OPTIONS] COMMAND [ARGS]...

Options

-v, --verbose#

-q, --quiet <quiet>#

--csv-field-size-limit <csv_field_size_limit>#: Increase the default limit for maximum field size. See https://docs.python.org/3/library/csv.html#csv.field_size_limit

-V, --version#: Show the version and exit.

Commands

dump: Dumps data to a SQL store

load: Loads data from a SQL store