mirror of
https://github.com/p2p-ld/nwb-linkml.git
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sneakers-the-rat
eac5ef4c80
move conftest to root so we find doctests? maybe we don't want to keep that tho
116 lines
2.7 KiB
Markdown
116 lines
2.7 KiB
Markdown
---
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file_format: mystnb
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#kernelspec:
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# name: nwb-linkml_docs
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mystnb:
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output_stderr: 'remove-warn'
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---
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# Quickstart
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## Reading Data
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To get the fun part out of the way, you can read ur data:
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```{code-cell}
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:tags: [hide-output]
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from pathlib import Path
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from rich.pretty import pprint, pretty_repr
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from rich.console import Console
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from nwb_linkml.io import HDF5IO
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# set up for pprinting in notebooks
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console = Console(width=100)
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print = console.print
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# find sample data file and read
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nwb_file = Path('../../nwb_linkml/tests/data/aibs.nwb')
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data = HDF5IO(nwb_file).read()
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print(data)
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```
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## Load and manipulate NWB schemas
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A {mod}`~nwb_linkml.providers.git` provider module can manage a repository to
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provide a given NWB namespace at a given version, and cast the
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schema into Pydantic models from {mod}`nwb_schema_language`.
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For the nwb-core schema, loading first just the namespaces file (without
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adjoining schema):
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```{code-cell}
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:tags: [hide-output]
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from nwb_linkml.providers.git import NWB_CORE_REPO
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from nwb_linkml.io.schema import load_namespaces
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namespace_file: 'Path' = NWB_CORE_REPO.provide_from_git('2.6.0')
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core_namespaces = load_namespaces(namespace_file)
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print(core_namespaces)
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```
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Or for a schema file...
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```{code-cell}
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:tags: [hide-output]
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from nwb_linkml.io.schema import load_schema_file
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base_schema_file = namespace_file.parent / 'nwb.base.yaml'
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nwb_core_base = load_schema_file(base_schema_file)
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print(nwb_core_base)
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```
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And additional {mod}`~nwb_linkml.adapters` are used to handle some of the
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implicit behavior in nwb schema files, like importing other namespaces
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at a specific version, and inter-schema class imports. Eg. the
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{class}`~nwb_linkml.adapters.NamespacesAdapter` finds the implicitly
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imported `hdmf-common` namespace (again provided by the git schema provider).
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```{code-cell}
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:tags: [hide-output]
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from nwb_linkml.adapters import NamespacesAdapter
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core_ns = NamespacesAdapter.from_yaml(namespace_file)
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print(core_ns.imported)
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```
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The classes in {mod}`nwb_schema_language` are just pydantic models, so they
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can be used like any other to create new, validated schemas.
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## Translating to LinkML
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{mod}`~nwb_linkml.adapters` handle the conversion from NWB schema language to
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LinkML.
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```{code-cell}
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:tags: [hide-output]
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core_linkml = core_ns.build()
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print(core_linkml)
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```
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The {class}`~nwb_linkml.adapters.BuildResult` class holds the LinkML representation
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of each of the schemas and their classes, which are now in {class}`linkml_runtime.linkml_model.SchemaDefinition`
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and `ClassDefinition` classes:
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```{code-cell}
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:tags: [hide-output]
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print(core_linkml.schemas[0])
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```
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## Generating Pydantic Models
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```{todo}
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Document Pydantic model generation
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```
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## Caching Output with Providers
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```{todo}
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Document provider usage
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```
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