nwb-linkml/docs/guide/quickstart.md

file_format	mystnb
mystnb	output_stderr remove-warn

Quickstart

Reading Data

To get the fun part out of the way, you can read ur data:

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from pathlib import Path
from rich.pretty import pprint, pretty_repr
from rich.console import Console
from nwb_linkml.io import HDF5IO

# set up for pprinting in notebooks
console = Console(width=100)
print = console.print

# find sample data file and read
nwb_file = Path('../../nwb_linkml/tests/data/aibs.nwb')
data = HDF5IO(nwb_file).read()
print(data) 

Load and manipulate NWB schemas

A {mod}~nwb_linkml.providers.git provider module can manage a repository to provide a given NWB namespace at a given version, and cast the schema into Pydantic models from {mod}nwb_schema_language.

For the nwb-core schema, loading first just the namespaces file (without adjoining schema):

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from nwb_linkml.providers.git import NWB_CORE_REPO
from nwb_linkml.io.schema import load_namespaces

namespace_file: 'Path' = NWB_CORE_REPO.provide_from_git('2.6.0')
core_namespaces = load_namespaces(namespace_file)
print(core_namespaces)

Or for a schema file...

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from nwb_linkml.io.schema import load_schema_file

base_schema_file =  namespace_file.parent / 'nwb.base.yaml'
nwb_core_base = load_schema_file(base_schema_file)
print(nwb_core_base)

And additional {mod}~nwb_linkml.adapters are used to handle some of the implicit behavior in nwb schema files, like importing other namespaces at a specific version, and inter-schema class imports. Eg. the {class}~nwb_linkml.adapters.NamespacesAdapter finds the implicitly imported hdmf-common namespace (again provided by the git schema provider).

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from nwb_linkml.adapters import NamespacesAdapter

core_ns = NamespacesAdapter.from_yaml(namespace_file)
print(core_ns.imported) 

The classes in {mod}nwb_schema_language are just pydantic models, so they can be used like any other to create new, validated schemas.

Translating to LinkML

{mod}~nwb_linkml.adapters handle the conversion from NWB schema language to LinkML.

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core_linkml = core_ns.build()
print(core_linkml)

The {class}~nwb_linkml.adapters.BuildResult class holds the LinkML representation of each of the schemas and their classes, which are now in {class}linkml_runtime.linkml_model.SchemaDefinition and ClassDefinition classes:

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print(core_linkml.schemas[0])

Generating Pydantic Models

Document Pydantic model generation

Caching Output with Providers

Document provider usage