linkml_store.api.stores.hdf5.hdf5_database module

class HDF5Database(handle=None, **kwargs)

Bases: Database

collection_class

alias of HDF5Collection

__init__(handle=None, **kwargs)

property file: File

commit(**kwargs)

Commit pending changes to the database.

Parameters:

kwargs

Returns:

close(**kwargs)

Close the database.

Parameters:

kwargs

Returns:

query(query, **kwargs)

Run a query against the database.

Examples

>>> from linkml_store.api.client import Client
>>> from linkml_store.api.queries import Query
>>> client = Client()
>>> db = client.attach_database("duckdb", alias="test")
>>> collection = db.create_collection("Person")
>>> collection.insert([{"id": "P1", "name": "John"}, {"id": "P2", "name": "Alice"}])
>>> query = Query(from_table="Person", where_clause={"name": "John"})
>>> result = db.query(query)
>>> len(result.rows)
1
>>> result.rows[0]["id"]
'P1'

type query:

Query

param query:

type kwargs:

param kwargs:

rtype:

QueryResult

return:

init_collections()

Initialize collections.

TODO: Not typically called directly: consider making this private :return:

induce_schema_view()

Induce a schema view from a schema definition.

>>> from linkml_store.api.client import Client
>>> from linkml_store.api.queries import Query
>>> client = Client()
>>> db = client.attach_database("duckdb", alias="test")
>>> collection = db.create_collection("Person")
>>> collection.insert([{"id": "P1", "name": "John", "age_in_years": 25},
...                 {"id": "P2", "name": "Alice", "age_in_years": 25}])
>>> schema_view = db.induce_schema_view()
>>> cd = schema_view.get_class("Person")
>>> cd.attributes["id"].range
'string'
>>> cd.attributes["age_in_years"].range
'integer'

Return type:

SchemaView

Returns:

A schema view