diff --git a/docs/notes/translation.md b/docs/notes/translation.md new file mode 100644 index 0000000..baddf3d --- /dev/null +++ b/docs/notes/translation.md @@ -0,0 +1,27 @@ +# translation + +what operations do we need when translating between schema languages? + +- Iteration - control over "for what" in the source or target domain. + eg. we need to map "all attributes and properties to slots" but then the + other direction of selection where we need to do one of everything per item + in the source domain as well +- dependence - source and target domain have different notions of linking +- level shifting - need to translate when something is a language-level + item to a schema-level item/object/class + + + +Steps: +- each namespaces or schema object creates one linkml schema file +- namespaces: one map, just imports all the other schema +- schema: actually create the object in the schema. + - Classes: + - Groups + - Enums (see below) + - Slots + - Attributes +- new files: files not in the source domain + - enum classes + +- Rename items \ No newline at end of file diff --git a/nwb_linkml/io.py b/nwb_linkml/io.py index e7d62cc..5768551 100644 --- a/nwb_linkml/io.py +++ b/nwb_linkml/io.py @@ -27,8 +27,6 @@ def load_yaml(path:Path) -> dict: # apply maps maps = [m for m in Map.instances if m.phase == PHASES.postload] - print('got maps') - print(maps) for amap in maps: ns_dict = amap.apply(ns_dict) return ns_dict diff --git a/nwb_linkml/linkml.py b/nwb_linkml/linkml.py new file mode 100644 index 0000000..6afdd04 --- /dev/null +++ b/nwb_linkml/linkml.py @@ -0,0 +1,3 @@ +from linkml.generators.linkmlgen import LinkmlGenerator +from linkml_runtime.linkml_model import SchemaDefinition +from linkml_runtime.dumpers import yaml_dumper diff --git a/nwb_linkml/maps/dataset.py b/nwb_linkml/maps/dataset.py new file mode 100644 index 0000000..e69de29 diff --git a/nwb_linkml/maps/namespace.py b/nwb_linkml/maps/namespace.py new file mode 100644 index 0000000..1df9bfc --- /dev/null +++ b/nwb_linkml/maps/namespace.py @@ -0,0 +1,29 @@ +""" +Practice translation of namespaces to linkml just as a warmup to +see what kind of operations we'll need + +Notes: + - Handling "namespace" imports within namespaces separately as prefixes +""" +from typing import List +from dataclasses import dataclass + + +from nwb_schema_language import Namespace +from linkml.utils.schema_builder import SchemaBuilder + +from linkml_runtime.linkml_model import SchemaDefinition + + + +# top-level attributes +def build_schema(namespace: Namespace) -> SchemaDefinition: + return SchemaDefinition( + id=namespace.name, + name=namespace.name, + title=namespace.full_name, + version=namespace.version, + imports=[schema.source for schema in namespace.schema_ if schema.source is not None] + ) + + diff --git a/nwb_linkml/maps/source.py b/nwb_linkml/maps/source.py new file mode 100644 index 0000000..6279182 --- /dev/null +++ b/nwb_linkml/maps/source.py @@ -0,0 +1,13 @@ +""" +Draft of a source to target mapping in pseudo-markup +""" + +namespace_map = { + "source": "Namespace", + "outputs": [ + {} + ], + "maps": [ + + ] +} diff --git a/nwb-schema-language/.cruft.json b/nwb_schema_language/.cruft.json similarity index 100% rename from nwb-schema-language/.cruft.json rename to nwb_schema_language/.cruft.json diff --git a/nwb-schema-language/.github/workflows/deploy-docs.yaml b/nwb_schema_language/.github/workflows/deploy-docs.yaml similarity index 100% rename from nwb-schema-language/.github/workflows/deploy-docs.yaml rename to nwb_schema_language/.github/workflows/deploy-docs.yaml diff --git a/nwb-schema-language/.github/workflows/main.yaml b/nwb_schema_language/.github/workflows/main.yaml similarity index 100% rename from nwb-schema-language/.github/workflows/main.yaml rename to nwb_schema_language/.github/workflows/main.yaml diff --git a/nwb-schema-language/.github/workflows/pypi-publish.yaml b/nwb_schema_language/.github/workflows/pypi-publish.yaml similarity index 100% rename from nwb-schema-language/.github/workflows/pypi-publish.yaml rename to nwb_schema_language/.github/workflows/pypi-publish.yaml diff --git a/nwb-schema-language/.gitignore b/nwb_schema_language/.gitignore similarity index 100% rename from nwb-schema-language/.gitignore rename to nwb_schema_language/.gitignore diff --git a/nwb-schema-language/CODE_OF_CONDUCT.md b/nwb_schema_language/CODE_OF_CONDUCT.md similarity index 100% rename from nwb-schema-language/CODE_OF_CONDUCT.md rename to nwb_schema_language/CODE_OF_CONDUCT.md diff --git a/nwb-schema-language/CONTRIBUTING.md b/nwb_schema_language/CONTRIBUTING.md similarity index 100% rename from nwb-schema-language/CONTRIBUTING.md rename to nwb_schema_language/CONTRIBUTING.md diff --git a/nwb-schema-language/LICENSE b/nwb_schema_language/LICENSE similarity index 100% rename from nwb-schema-language/LICENSE rename to nwb_schema_language/LICENSE diff --git a/nwb-schema-language/Makefile b/nwb_schema_language/Makefile similarity index 100% rename from nwb-schema-language/Makefile rename to nwb_schema_language/Makefile diff --git a/nwb-schema-language/README.md b/nwb_schema_language/README.md similarity index 100% rename from nwb-schema-language/README.md rename to nwb_schema_language/README.md diff --git a/nwb-schema-language/about.yaml b/nwb_schema_language/about.yaml similarity index 100% rename from nwb-schema-language/about.yaml rename to nwb_schema_language/about.yaml diff --git a/nwb-schema-language/config.env b/nwb_schema_language/config.env similarity index 100% rename from nwb-schema-language/config.env rename to nwb_schema_language/config.env diff --git a/nwb-schema-language/config.yaml b/nwb_schema_language/config.yaml similarity index 100% rename from nwb-schema-language/config.yaml rename to nwb_schema_language/config.yaml diff --git a/nwb-schema-language/mkdocs.yml b/nwb_schema_language/mkdocs.yml similarity index 100% rename from nwb-schema-language/mkdocs.yml rename to nwb_schema_language/mkdocs.yml diff --git a/nwb-schema-language/poetry.lock b/nwb_schema_language/poetry.lock similarity index 100% rename from nwb-schema-language/poetry.lock rename to nwb_schema_language/poetry.lock diff --git a/nwb-schema-language/project.Makefile b/nwb_schema_language/project.Makefile similarity index 100% rename from nwb-schema-language/project.Makefile rename to nwb_schema_language/project.Makefile diff --git a/nwb-schema-language/project/excel/nwb_schema_language.xlsx b/nwb_schema_language/project/excel/nwb_schema_language.xlsx similarity index 100% rename from nwb-schema-language/project/excel/nwb_schema_language.xlsx rename to nwb_schema_language/project/excel/nwb_schema_language.xlsx diff --git a/nwb-schema-language/project/graphql/nwb_schema_language.graphql b/nwb_schema_language/project/graphql/nwb_schema_language.graphql similarity index 100% rename from nwb-schema-language/project/graphql/nwb_schema_language.graphql rename to nwb_schema_language/project/graphql/nwb_schema_language.graphql diff 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a/nwb-schema-language/project/owl/nwb_schema_language.owl.ttl b/nwb_schema_language/project/owl/nwb_schema_language.owl.ttl similarity index 100% rename from nwb-schema-language/project/owl/nwb_schema_language.owl.ttl rename to nwb_schema_language/project/owl/nwb_schema_language.owl.ttl diff --git a/nwb-schema-language/project/prefixmap/nwb_schema_language.yaml b/nwb_schema_language/project/prefixmap/nwb_schema_language.yaml similarity index 100% rename from nwb-schema-language/project/prefixmap/nwb_schema_language.yaml rename to nwb_schema_language/project/prefixmap/nwb_schema_language.yaml diff --git a/nwb-schema-language/project/protobuf/nwb_schema_language.proto b/nwb_schema_language/project/protobuf/nwb_schema_language.proto similarity index 100% rename from nwb-schema-language/project/protobuf/nwb_schema_language.proto rename to nwb_schema_language/project/protobuf/nwb_schema_language.proto diff --git a/nwb-schema-language/project/shacl/nwb_schema_language.shacl.ttl b/nwb_schema_language/project/shacl/nwb_schema_language.shacl.ttl similarity index 100% rename from nwb-schema-language/project/shacl/nwb_schema_language.shacl.ttl rename to nwb_schema_language/project/shacl/nwb_schema_language.shacl.ttl diff --git a/nwb-schema-language/project/shex/nwb_schema_language.shex b/nwb_schema_language/project/shex/nwb_schema_language.shex similarity index 100% rename from nwb-schema-language/project/shex/nwb_schema_language.shex rename to nwb_schema_language/project/shex/nwb_schema_language.shex diff --git a/nwb-schema-language/project/sqlschema/nwb_schema_language.sql b/nwb_schema_language/project/sqlschema/nwb_schema_language.sql similarity index 100% rename from nwb-schema-language/project/sqlschema/nwb_schema_language.sql rename to nwb_schema_language/project/sqlschema/nwb_schema_language.sql diff --git a/nwb-schema-language/pyproject.toml b/nwb_schema_language/pyproject.toml similarity index 100% rename from nwb-schema-language/pyproject.toml rename to nwb_schema_language/pyproject.toml diff --git a/nwb-schema-language/src/data/tests/nwb.base.yaml b/nwb_schema_language/src/data/tests/nwb.base.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.base.yaml rename to nwb_schema_language/src/data/tests/nwb.base.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.behavior.yaml b/nwb_schema_language/src/data/tests/nwb.behavior.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.behavior.yaml rename to nwb_schema_language/src/data/tests/nwb.behavior.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.device.yaml b/nwb_schema_language/src/data/tests/nwb.device.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.device.yaml rename to nwb_schema_language/src/data/tests/nwb.device.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.ecephys.yaml b/nwb_schema_language/src/data/tests/nwb.ecephys.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.ecephys.yaml rename to nwb_schema_language/src/data/tests/nwb.ecephys.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.epoch.yaml b/nwb_schema_language/src/data/tests/nwb.epoch.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.epoch.yaml rename to nwb_schema_language/src/data/tests/nwb.epoch.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.file.yaml b/nwb_schema_language/src/data/tests/nwb.file.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.file.yaml rename to nwb_schema_language/src/data/tests/nwb.file.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.icephys.yaml b/nwb_schema_language/src/data/tests/nwb.icephys.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.icephys.yaml rename to nwb_schema_language/src/data/tests/nwb.icephys.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.image.yaml b/nwb_schema_language/src/data/tests/nwb.image.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.image.yaml rename to nwb_schema_language/src/data/tests/nwb.image.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.misc.yaml b/nwb_schema_language/src/data/tests/nwb.misc.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.misc.yaml rename to nwb_schema_language/src/data/tests/nwb.misc.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.namespace.yaml b/nwb_schema_language/src/data/tests/nwb.namespace.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.namespace.yaml rename to nwb_schema_language/src/data/tests/nwb.namespace.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.ogen.yaml b/nwb_schema_language/src/data/tests/nwb.ogen.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.ogen.yaml rename to nwb_schema_language/src/data/tests/nwb.ogen.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.ophys.yaml b/nwb_schema_language/src/data/tests/nwb.ophys.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.ophys.yaml rename to nwb_schema_language/src/data/tests/nwb.ophys.yaml diff --git a/nwb-schema-language/src/data/tests/nwb.retinotopy.yaml b/nwb_schema_language/src/data/tests/nwb.retinotopy.yaml similarity index 100% rename from nwb-schema-language/src/data/tests/nwb.retinotopy.yaml rename to nwb_schema_language/src/data/tests/nwb.retinotopy.yaml diff --git a/nwb-schema-language/src/docs/about.md b/nwb_schema_language/src/docs/about.md similarity index 100% rename from nwb-schema-language/src/docs/about.md rename to nwb_schema_language/src/docs/about.md diff --git a/nwb-schema-language/src/nwb_schema_language/__init__.py b/nwb_schema_language/src/nwb_schema_language/__init__.py similarity index 100% rename from nwb-schema-language/src/nwb_schema_language/__init__.py rename to nwb_schema_language/src/nwb_schema_language/__init__.py diff --git a/nwb-schema-language/src/nwb_schema_language/_version.py b/nwb_schema_language/src/nwb_schema_language/_version.py similarity index 100% rename from nwb-schema-language/src/nwb_schema_language/_version.py rename to nwb_schema_language/src/nwb_schema_language/_version.py diff --git a/nwb-schema-language/src/nwb_schema_language/datamodel/__init__.py b/nwb_schema_language/src/nwb_schema_language/datamodel/__init__.py similarity index 100% rename from nwb-schema-language/src/nwb_schema_language/datamodel/__init__.py rename to nwb_schema_language/src/nwb_schema_language/datamodel/__init__.py diff --git a/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_language.py b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py similarity index 99% rename from nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_language.py rename to nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py index f010dc6..a9bb3ef 100644 --- a/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_language.py +++ b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py @@ -1,9 +1,9 @@ # Auto generated from nwb_schema_language.yaml by pythongen.py version: 0.0.1 # Generation date: 2023-08-18T00:36:55 -# Schema: nwb-schema-language +# Schema: nwb_schema_language # # id: https://w3id.org/p2p_ld/nwb-schema-language -# description: Translation of the nwb-schema-language to LinkML +# description: Translation of the nwb_schema_language to LinkML # license: GNU GPL v3.0 import dataclasses diff --git a/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py similarity index 100% rename from nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py rename to nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py diff --git a/nwb_schema_language/src/nwb_schema_language/datamodel/schemaview.py b/nwb_schema_language/src/nwb_schema_language/datamodel/schemaview.py new file mode 100644 index 0000000..593d3a6 --- /dev/null +++ b/nwb_schema_language/src/nwb_schema_language/datamodel/schemaview.py @@ -0,0 +1,7 @@ +from pathlib import Path +from linkml_runtime.utils.schemaview import SchemaView + +SCHEMA_FILE = Path(__file__).parent.parent.resolve() / 'schema' / 'nwb_schema_language.yaml' + +schema_view = SchemaView(SCHEMA_FILE) + diff --git a/nwb-schema-language/src/nwb_schema_language/patches.py b/nwb_schema_language/src/nwb_schema_language/patches.py similarity index 100% rename from nwb-schema-language/src/nwb_schema_language/patches.py rename to nwb_schema_language/src/nwb_schema_language/patches.py diff --git a/nwb-schema-language/src/nwb_schema_language/schema/nwb_schema_language.yaml b/nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml similarity index 100% rename from nwb-schema-language/src/nwb_schema_language/schema/nwb_schema_language.yaml rename to nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml diff --git a/nwb-schema-language/tests/__init__.py b/nwb_schema_language/tests/__init__.py similarity index 100% rename from nwb-schema-language/tests/__init__.py rename to nwb_schema_language/tests/__init__.py diff --git a/nwb-schema-language/tests/test_data.py b/nwb_schema_language/tests/test_data.py similarity index 100% rename from nwb-schema-language/tests/test_data.py rename to nwb_schema_language/tests/test_data.py diff --git a/nwb-schema-language/utils/get-value.sh b/nwb_schema_language/utils/get-value.sh similarity index 100% rename from nwb-schema-language/utils/get-value.sh rename to nwb_schema_language/utils/get-value.sh diff --git a/poetry.lock b/poetry.lock index c408568..9ee4c88 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,29 @@ # This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +[[package]] +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" +optional = false +python-versions = "*" +files = [ + {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, +] + +[[package]] +name = "arrow" +version = "1.2.3" +description = "Better dates & times for Python" +optional = false +python-versions = ">=3.6" +files = [ + {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, + {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, +] + +[package.dependencies] +python-dateutil = ">=2.7.0" + [[package]] name = "attrs" version = "23.1.0" @@ -29,6 +53,30 @@ files = [ {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, ] +[[package]] +name = "cfgraph" +version = "0.2.1" +description = "rdflib collections flattening graph" +optional = false +python-versions = "*" +files = [ + {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"}, +] + +[package.dependencies] +rdflib = ">=0.4.2" + +[[package]] +name = "chardet" +version = "5.2.0" +description = "Universal encoding detector for Python 3" +optional = false +python-versions = ">=3.7" +files = [ + {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, + {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, +] + [[package]] name = "charset-normalizer" version = "3.2.0" @@ -162,6 +210,17 @@ pandas = ["pandas"] rdflib = ["rdflib"] tests = ["coverage", "pytest"] +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +optional = false +python-versions = ">=3.5" +files = [ + {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"}, + {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, +] + [[package]] name = "deprecated" version = "1.2.14" @@ -179,6 +238,44 @@ wrapt = ">=1.10,<2" [package.extras] dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] +[[package]] +name = "et-xmlfile" +version = "1.1.0" +description = "An implementation of lxml.xmlfile for the standard library" +optional = false +python-versions = ">=3.6" +files = [ + {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"}, + {file = "et_xmlfile-1.1.0.tar.gz", hash = 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"32b9026599bc647c7c91a582f2629cd4bf23ca6bbedecd62ac455cfde4c8ed5c" +content-hash = "90f5eaedd0572c26dfac8a9f2fed0c8ec50f70a54b7bff03a43816f96cb60bb1" diff --git a/pyproject.toml b/pyproject.toml index 5e84214..b4d79aa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,18 +7,25 @@ license = "GPL-3.0" readme = "README.md" packages = [ {include = "nwb_linkml"}, -# {include = "nwb_schema_language", from="nwb-schema-language/src"} + {include = "nwb_schema_language", from="nwb_schema_language/src"} ] [tool.poetry.dependencies] python = "^3.11" pyyaml = "^6.0" linkml-runtime = "^1.5.6" -nwb_schema_language = { path = './nwb-schema-language', develop = true } +nwb_schema_language = { path = './nwb_schema_language', develop = true } pydantic = "<2" rich = "^13.5.2" +linkml = "^1.5.7" +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.0" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" + + +[tool.pytest.ini_options] diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/fixtures.py b/tests/fixtures.py new file mode 100644 index 0000000..872193a --- /dev/null +++ b/tests/fixtures.py @@ -0,0 +1,22 @@ +import pytest +from typing import Dict + + +from nwb_linkml import io +import shutil +from pathlib import Path + +@pytest.fixture(scope="session") +def tmp_output_dir() -> Path: + path = Path(__file__).parent.resolve() / '__tmp__' + if path.exists(): + shutil.rmtree(str(path)) + path.mkdir() + + return path + + +@pytest.fixture(scope="session") +def nwb_core_fixture() -> Dict[str, io.NamespaceBundle]: + nwb_core = io.load_nwb_core() + return nwb_core \ No newline at end of file diff --git a/tests/test_namespace.py b/tests/test_namespace.py new file mode 100644 index 0000000..0e54d9a --- /dev/null +++ b/tests/test_namespace.py @@ -0,0 +1,13 @@ +import pytest + +from .fixtures import nwb_core_fixture, tmp_output_dir + +from nwb_linkml.maps.namespace import build_schema +from linkml_runtime.dumpers import yaml_dumper + +def test_namespace_to_linkml(nwb_core_fixture, tmp_output_dir): + output_file = tmp_output_dir / 'nwb.namespace.yml' + schema = build_schema(nwb_core_fixture['nwb-core']['namespace'].namespaces[0]) + + yaml_dumper.dump(schema, output_file) +