SQLStore#

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

A wrapper for a SQLite 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 | None[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) → YAMLRoot | list[linkml_runtime.utils.yamlutils.YAMLRoot] | None[source]#

Translate from SQLAlchemy declarative module to native LinkML

Parameters:

obj – sqla object

Returns:

native dataclass object

load(target_class: str | type[linkml_runtime.utils.yamlutils.YAMLRoot] = None) → YAMLRoot[source]#

Loads a LinkML object from the wrapped SQLite database

Parameters:

target_class –

Returns:

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

Translate native LinkML object to SQLAlchemy declarative module

Parameters:

obj –

Returns:

use_memory: bool = False#

//docs.sqlalchemy.org/en/20/dialects/sqlite.html#using-a-memory-database-in-multiple-threads

Type:

https

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