From 5c69c48f354b032c84624b82da65155d4814732b Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Wed, 16 Aug 2023 16:07:36 -0700 Subject: [PATCH] make linkml cookiecutter --- nwb-schema-linkml/.cruft.json | 27 + .../.github/workflows/deploy-docs.yaml | 35 + nwb-schema-linkml/.github/workflows/main.yaml | 37 + .../.github/workflows/pypi-publish.yaml | 40 + nwb-schema-linkml/.gitignore | 133 + nwb-schema-linkml/CODE_OF_CONDUCT.md | 76 + nwb-schema-linkml/CONTRIBUTING.md | 73 + nwb-schema-linkml/LICENSE | 675 +++++ nwb-schema-linkml/Makefile | 190 ++ nwb-schema-linkml/README.md | 33 + nwb-schema-linkml/about.yaml | 7 + nwb-schema-linkml/config.env | 8 + nwb-schema-linkml/config.yaml | 41 + .../examples/Namespaces-001.yaml | 7 + nwb-schema-linkml/examples/README.md | 5 + nwb-schema-linkml/mkdocs.yml | 25 + nwb-schema-linkml/poetry.lock | 2521 +++++++++++++++++ nwb-schema-linkml/project.Makefile | 1 + .../project/excel/nwb_schema_language.xlsx | Bin 0 -> 5947 bytes .../graphql/nwb_schema_language.graphql | 23 + .../jsonld/nwb_schema_language.context.jsonld | 51 + .../project/jsonld/nwb_schema_language.jsonld | 543 ++++ .../nwb_schema_language.schema.json | 161 ++ .../project/owl/nwb_schema_language.owl.ttl | 343 +++ .../prefixmap/nwb_schema_language.yaml | 11 + .../protobuf/nwb_schema_language.proto | 23 + .../shacl/nwb_schema_language.shacl.ttl | 164 ++ .../project/shex/nwb_schema_language.shex | 74 + .../project/sqlschema/nwb_schema_language.sql | 24 + nwb-schema-linkml/pyproject.toml | 30 + .../src/data/examples/Namespaces-001.yaml | 7 + nwb-schema-linkml/src/docs/about.md | 3 + .../src/nwb_schema_language/_version.py | 7 + .../nwb_schema_language/datamodel/__init__.py | 1 + .../datamodel/nwb_schema_language.py | 193 ++ .../schema/nwb_schema_language.yaml | 96 + nwb-schema-linkml/tests/__init__.py | 1 + nwb-schema-linkml/tests/test_data.py | 22 + nwb-schema-linkml/utils/get-value.sh | 4 + 39 files changed, 5715 insertions(+) create mode 100644 nwb-schema-linkml/.cruft.json create mode 100644 nwb-schema-linkml/.github/workflows/deploy-docs.yaml create mode 100644 nwb-schema-linkml/.github/workflows/main.yaml create mode 100644 nwb-schema-linkml/.github/workflows/pypi-publish.yaml create mode 100644 nwb-schema-linkml/.gitignore create mode 100644 nwb-schema-linkml/CODE_OF_CONDUCT.md create mode 100644 nwb-schema-linkml/CONTRIBUTING.md create mode 100644 nwb-schema-linkml/LICENSE create mode 100644 nwb-schema-linkml/Makefile create mode 100644 nwb-schema-linkml/README.md create mode 100644 nwb-schema-linkml/about.yaml create mode 100644 nwb-schema-linkml/config.env create mode 100644 nwb-schema-linkml/config.yaml create mode 100644 nwb-schema-linkml/examples/Namespaces-001.yaml create mode 100644 nwb-schema-linkml/examples/README.md create mode 100644 nwb-schema-linkml/mkdocs.yml create mode 100644 nwb-schema-linkml/poetry.lock create mode 100644 nwb-schema-linkml/project.Makefile create mode 100644 nwb-schema-linkml/project/excel/nwb_schema_language.xlsx create mode 100644 nwb-schema-linkml/project/graphql/nwb_schema_language.graphql create mode 100644 nwb-schema-linkml/project/jsonld/nwb_schema_language.context.jsonld create mode 100644 nwb-schema-linkml/project/jsonld/nwb_schema_language.jsonld create mode 100644 nwb-schema-linkml/project/jsonschema/nwb_schema_language.schema.json create mode 100644 nwb-schema-linkml/project/owl/nwb_schema_language.owl.ttl create mode 100644 nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml create mode 100644 nwb-schema-linkml/project/protobuf/nwb_schema_language.proto create mode 100644 nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl create mode 100644 nwb-schema-linkml/project/shex/nwb_schema_language.shex create mode 100644 nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql create mode 100644 nwb-schema-linkml/pyproject.toml create mode 100644 nwb-schema-linkml/src/data/examples/Namespaces-001.yaml create mode 100644 nwb-schema-linkml/src/docs/about.md create mode 100644 nwb-schema-linkml/src/nwb_schema_language/_version.py create mode 100644 nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py create mode 100644 nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py create mode 100644 nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml create mode 100644 nwb-schema-linkml/tests/__init__.py create mode 100644 nwb-schema-linkml/tests/test_data.py create mode 100644 nwb-schema-linkml/utils/get-value.sh diff --git a/nwb-schema-linkml/.cruft.json b/nwb-schema-linkml/.cruft.json new file mode 100644 index 0000000..65da624 --- /dev/null +++ b/nwb-schema-linkml/.cruft.json @@ -0,0 +1,27 @@ +{ + "template": "https://github.com/linkml/linkml-project-cookiecutter", + "commit": "ef7ff16925321a2abdbaa5a2ba5db8aa83ebf24f", + "checkout": null, + "context": { + "cookiecutter": { + "project_name": "nwb-schema-language", + "__project_slug": "nwb_schema_language", + "github_org": "p2p_ld", + "__source_path": "src/nwb_schema_language/schema/nwb_schema_language.yaml", + "project_description": "Translation of the nwb-schema-language to LinkML", + "full_name": "Jonny Saunders", + "email": "j@nny.fyi", + "__author": "Jonny Saunders ", + "license": "GNU GPL v3.0", + "main_schema_class": "Namespaces", + "create_python_classes": "Yes", + "use_schemasheets": "No", + "google_sheet_id": "1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ", + "google_sheet_tabs": "personinfo enums", + "__google_sheet_module": "personinfo_enums", + "github_token_for_pypi_deployment": "PYPI_PASSWORD", + "_template": "https://github.com/linkml/linkml-project-cookiecutter" + } + }, + "directory": null +} diff --git a/nwb-schema-linkml/.github/workflows/deploy-docs.yaml b/nwb-schema-linkml/.github/workflows/deploy-docs.yaml new file mode 100644 index 0000000..6d90198 --- /dev/null +++ b/nwb-schema-linkml/.github/workflows/deploy-docs.yaml @@ -0,0 +1,35 @@ +--- +name: Auto-deployment of nwb_schema_language Documentation +on: + push: + branches: [main] + +jobs: + build-docs: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + with: + fetch-depth: 0 # otherwise, you will failed to push refs to dest repo + + - name: Set up Python 3. + uses: actions/setup-python@v4 + with: + python-version: 3.9 + + - name: Install Poetry. + uses: snok/install-poetry@v1.3 + + - name: Install dependencies. + run: poetry install -E docs + + - name: Build documentation. + run: | + mkdir -p docs + touch docs/.nojekyll + make gendoc + ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true + make mkd-gh-deploy + +... diff --git a/nwb-schema-linkml/.github/workflows/main.yaml b/nwb-schema-linkml/.github/workflows/main.yaml new file mode 100644 index 0000000..aea1428 --- /dev/null +++ b/nwb-schema-linkml/.github/workflows/main.yaml @@ -0,0 +1,37 @@ +# Built from: +# https://docs.github.com/en/actions/guides/building-and-testing-python +# https://github.com/snok/install-poetry#workflows-and-tips +--- +name: Build and test nwb_schema_language + +on: [pull_request] + +jobs: + test: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.9", "3.10"] + + steps: + + - name: Check out repository + uses: actions/checkout@v3 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Install Poetry + uses: snok/install-poetry@v1.3 + + - name: Install dependencies + run: poetry install --no-interaction --no-root + + - name: Install project + run: poetry install --no-interaction + + - name: Run test suite + run: make test diff --git a/nwb-schema-linkml/.github/workflows/pypi-publish.yaml b/nwb-schema-linkml/.github/workflows/pypi-publish.yaml new file mode 100644 index 0000000..512fb4b --- /dev/null +++ b/nwb-schema-linkml/.github/workflows/pypi-publish.yaml @@ -0,0 +1,40 @@ +--- +name: Publish Python Package + +on: + release: + types: [created] + +jobs: + build-n-publish: + name: Build and publish Python 🐍 distributions 📦 to PyPI + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: 3.9 + + - name: Install Poetry + run: | + pip install poetry + poetry self add "poetry-dynamic-versioning[plugin]" + # uses: snok/install-poetry@v1.1.6 + # with: + # virtualenvs-create: true + # virtualenvs-in-project: true + + # - name: Install dependencies + # run: poetry install --no-interaction + + - name: Build source and wheel archives + run: poetry build + + - name: Publish distribution 📦 to PyPI + uses: pypa/gh-action-pypi-publish@v1.2.2 + with: + user: __token__ + password: ${{ secrets.PYPI_PASSWORD }} diff --git a/nwb-schema-linkml/.gitignore b/nwb-schema-linkml/.gitignore new file mode 100644 index 0000000..e110be5 --- /dev/null +++ b/nwb-schema-linkml/.gitignore @@ -0,0 +1,133 @@ +/docs/ +/project/docs/ +/tmp/ + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ diff --git a/nwb-schema-linkml/CODE_OF_CONDUCT.md b/nwb-schema-linkml/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..2b301c6 --- /dev/null +++ b/nwb-schema-linkml/CODE_OF_CONDUCT.md @@ -0,0 +1,76 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to make participation in our project and +our community a harassment-free experience for everyone, regardless of age, +body size, disability, ethnicity, gender identity and expression, level of +experience, nationality, personal appearance, race, religion, or sexual +identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an +appointed representative at an online or offline event. Representation of a +project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by [contacting the project team](contact.md). All complaints will be +reviewed and investigated and will result in a response that is deemed +necessary and appropriate to the circumstances. The project team is obligated +to maintain confidentiality with regard to the reporter of an incident. Further +details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This code of conduct has been derived from the excellent code of conduct of the +[ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md) +which in turn is adapted from the [Contributor Covenant][homepage], version +1.4, available at [https://contributor-covenant.org/version/1/4][version] + +[homepage]: https://contributor-covenant.org +[version]: https://contributor-covenant.org/version/1/4/ diff --git a/nwb-schema-linkml/CONTRIBUTING.md b/nwb-schema-linkml/CONTRIBUTING.md new file mode 100644 index 0000000..c61b7b0 --- /dev/null +++ b/nwb-schema-linkml/CONTRIBUTING.md @@ -0,0 +1,73 @@ +# Contributing to nwb-schema-language + +:+1: First of all: Thank you for taking the time to contribute! + +The following is a set of guidelines for contributing to +nwb-schema-language. These guidelines are not strict rules. +Use your best judgment, and feel free to propose changes to this document +in a pull request. + +## Table Of Contents + +* [Code of Conduct](#code-of-conduct) +* [Guidelines for Contributions and Requests](#contributions) + * [Reporting problems with the data model](#reporting-bugs) + * [Requesting new terms](#requesting-terms) + * [Adding new terms yourself](#adding-terms) +* [Best Practices](#best-practices) + * [How to write a great issue](#great-issues) + * [How to create a great pull/merge request](#great-pulls) + + + +## Code of Conduct + +The nwb-schema-language team strives to create a +welcoming environment for editors, users and other contributors. +Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md). + + + +## Guidelines for Contributions and Requests + + + +### Reporting problems with the data model + +Please use our [Issue Tracker][issues] to report problems with the ontology. + + + +### Requesting new terms + +Please use our [Issue Tracker][issues] to request a new term for the ontology. + + + +### Adding new terms yourself + +Please submit a [Pull Request][pulls] to submit a new term for consideration. + + + +## Best Practices + + + +### How to write a great issue + +Please review GitHub's overview article, +["Tracking Your Work with Issues"][about-issues]. + + + +### How to create a great pull/merge request + +Please review GitHub's article, ["About Pull Requests"][about-pulls], +and make your changes on a [new branch][about-branches]. + +[about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches +[about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues +[about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests +[issues]: https://github.com/p2p_ld/nwb-schema-language/issues/ +[pulls]: https://github.com/p2p_ld/nwb-schema-language/pulls/ diff --git a/nwb-schema-linkml/LICENSE b/nwb-schema-linkml/LICENSE new file mode 100644 index 0000000..a737dcf --- /dev/null +++ b/nwb-schema-linkml/LICENSE @@ -0,0 +1,675 @@ + + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/nwb-schema-linkml/Makefile b/nwb-schema-linkml/Makefile new file mode 100644 index 0000000..88f65f3 --- /dev/null +++ b/nwb-schema-linkml/Makefile @@ -0,0 +1,190 @@ +MAKEFLAGS += --warn-undefined-variables +SHELL := bash +.SHELLFLAGS := -eu -o pipefail -c +.DEFAULT_GOAL := help +.DELETE_ON_ERROR: +.SUFFIXES: +.SECONDARY: + +RUN = poetry run +# get values from about.yaml file +SCHEMA_NAME = $(shell ${SHELL} ./utils/get-value.sh name) +SOURCE_SCHEMA_PATH = $(shell ${SHELL} ./utils/get-value.sh source_schema_path) +SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH)) +SRC = src +DEST = project +PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel +DOCDIR = docs +EXAMPLEDIR = examples +SHEET_MODULE = personinfo_enums +SHEET_ID = $(shell ${SHELL} ./utils/get-value.sh google_sheet_id) +SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs) +SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml + +# environment variables +include config.env + +GEN_PARGS = +ifdef LINKML_GENERATORS_PROJECT_ARGS +GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS} +endif + +GEN_DARGS = +ifdef LINKML_GENERATORS_MARKDOWN_ARGS +GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS} +endif + + +# basename of a YAML file in model/ +.PHONY: all clean + +# note: "help" MUST be the first target in the file, +# when the user types "make" they should get help info +help: status + @echo "" + @echo "make setup -- initial setup (run this first)" + @echo "make site -- makes site locally" + @echo "make install -- install dependencies" + @echo "make test -- runs tests" + @echo "make lint -- perform linting" + @echo "make testdoc -- builds docs and runs local test server" + @echo "make deploy -- deploys site" + @echo "make update -- updates linkml version" + @echo "make help -- show this help" + @echo "" + +status: check-config + @echo "Project: $(SCHEMA_NAME)" + @echo "Source: $(SOURCE_SCHEMA_PATH)" + +# generate products and add everything to github +setup: install gen-project gen-examples gendoc git-init-add + +# install any dependencies required for building +install: + git init + poetry install +.PHONY: install + +# --- +# Project Synchronization +# --- +# +# check we are up to date +check: cruft-check +cruft-check: + cruft check +cruft-diff: + cruft diff + +update: update-template update-linkml +update-template: + cruft update + +# todo: consider pinning to template +update-linkml: + poetry add -D linkml@latest + +# EXPERIMENTAL +create-data-harmonizer: + npm init data-harmonizer $(SOURCE_SCHEMA_PATH) + +all: site +site: gen-project gendoc +%.yaml: gen-project +deploy: all mkd-gh-deploy + +compile-sheets: + $(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH) + +# In future this will be done by conversion +gen-examples: + cp src/data/examples/* $(EXAMPLEDIR) + +# generates all project files + +gen-project: $(PYMODEL) + $(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL) + + +test: test-schema test-python test-examples + +test-schema: + $(RUN) gen-project ${GEN_PARGS} -d tmp $(SOURCE_SCHEMA_PATH) + +test-python: + $(RUN) python -m unittest discover + +lint: + $(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) + +check-config: + @(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n - Remember to edit 'about.yaml'\n\n" || exit 0) + +convert-examples-to-%: + $(patsubst %, $(RUN) linkml-convert % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.yaml")) + +examples/%.yaml: src/data/examples/%.yaml + $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ +examples/%.json: src/data/examples/%.yaml + $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ +examples/%.ttl: src/data/examples/%.yaml + $(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ + +test-examples: examples/output + +examples/output: src/nwb_schema_language/schema/nwb_schema_language.yaml + mkdir -p $@ + $(RUN) linkml-run-examples \ + --output-formats json \ + --output-formats yaml \ + --counter-example-input-directory src/data/examples/invalid \ + --input-directory src/data/examples/valid \ + --output-directory $@ \ + --schema $< > $@/README.md + +# Test documentation locally +serve: mkd-serve + +# Python datamodel +$(PYMODEL): + mkdir -p $@ + + +$(DOCDIR): + mkdir -p $@ + +gendoc: $(DOCDIR) + cp $(SRC)/docs/*md $(DOCDIR) ; \ + $(RUN) gen-doc ${GEN_DARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) + +testdoc: gendoc serve + +MKDOCS = $(RUN) mkdocs +mkd-%: + $(MKDOCS) $* + +PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel +git-init-add: git-init git-add git-commit git-status +git-init: + git init +git-add: .cruft.json + git add .gitignore .github .cruft.json Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/nwb_schema_language/schema/*yaml src/*/datamodel/*py src/data src/docs tests src/*/_version.py + git add $(patsubst %, project/%, $(PROJECT_FOLDERS)) +git-commit: + git commit -m 'chore: initial commit' -a +git-status: + git status + +# only necessary if setting up via cookiecutter +.cruft.json: + echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \ + touch $@ + +clean: + rm -rf $(DEST) + rm -rf tmp + rm -fr docs/* + rm -fr $(PYMODEL)/* + +include project.Makefile diff --git a/nwb-schema-linkml/README.md b/nwb-schema-linkml/README.md new file mode 100644 index 0000000..c393a11 --- /dev/null +++ b/nwb-schema-linkml/README.md @@ -0,0 +1,33 @@ +# nwb-schema-language + +Translation of the nwb-schema-language to LinkML + +## Website + +[https://p2p_ld.github.io/nwb-schema-language](https://p2p_ld.github.io/nwb-schema-language) + +## Repository Structure + +* [examples/](examples/) - example data +* [project/](project/) - project files (do not edit these) +* [src/](src/) - source files (edit these) + * [nwb_schema_language](src/nwb_schema_language) + * [schema](src/nwb_schema_language/schema) -- LinkML schema + (edit this) + * [datamodel](src/nwb_schema_language/datamodel) -- generated + Python datamodel +* [tests/](tests/) - Python tests + +## Developer Documentation + +
+Use the `make` command to generate project artefacts: + +* `make all`: make everything +* `make deploy`: deploys site +
+ +## Credits + +This project was made with +[linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter). diff --git a/nwb-schema-linkml/about.yaml b/nwb-schema-linkml/about.yaml new file mode 100644 index 0000000..6a10bbe --- /dev/null +++ b/nwb-schema-linkml/about.yaml @@ -0,0 +1,7 @@ +--- +name: nwb_schema_language +author: Jonny Saunders +description: Translation of the nwb-schema-language to LinkML +source_schema_path: src/nwb_schema_language/schema/nwb_schema_language.yaml +google_sheet_id: 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ +google_sheet_tabs: personinfo enums diff --git a/nwb-schema-linkml/config.env b/nwb-schema-linkml/config.env new file mode 100644 index 0000000..54866fa --- /dev/null +++ b/nwb-schema-linkml/config.env @@ -0,0 +1,8 @@ +LINKML_GENERATORS_PROJECT_ARGS=--config-file config.yaml --exclude owl --exclude shacl + +### Extra layer of configuration for Makefile beyond +### what 'gen-project --config-file config.yaml' provides. +### Uncomment and set environment variables as needed. + +# LINKML_GENERATORS_MARKDOWN_ARGS=--no-mergeimports + diff --git a/nwb-schema-linkml/config.yaml b/nwb-schema-linkml/config.yaml new file mode 100644 index 0000000..56da66d --- /dev/null +++ b/nwb-schema-linkml/config.yaml @@ -0,0 +1,41 @@ +# Configuration of generators (defaults illustrated) +--- +generator_args: + excel: + mergeimports: true + owl: + mergeimports: true + metaclasses: true + type_objects: true + # throws 'Cannot handle metadata profile: rdfs' + # metadata_profile: rdfs + markdown: + mergeimports: true + graphql: + mergeimports: true + java: + mergeimports: true + metadata: true + jsonld: + mergeimports: true + jsonschema: + mergeimports: true + jsonldcontext: + mergeimports: true + python: + mergeimports: true + prefixmap: + mergeimports: true + proto: + mergeimports: true + shacl: + mergeimports: true + shex: + mergeimports: true + sqlddl: + mergeimports: true + typescript: + mergeimports: true + metadata: true + +... diff --git a/nwb-schema-linkml/examples/Namespaces-001.yaml b/nwb-schema-linkml/examples/Namespaces-001.yaml new file mode 100644 index 0000000..2f8802f --- /dev/null +++ b/nwb-schema-linkml/examples/Namespaces-001.yaml @@ -0,0 +1,7 @@ +# Example data object +--- +entries: + - id: example:Namespaces001 + name: foo bar + primary_email: foo.bar@example.com + age_in_years: 33 diff --git a/nwb-schema-linkml/examples/README.md b/nwb-schema-linkml/examples/README.md new file mode 100644 index 0000000..f202941 --- /dev/null +++ b/nwb-schema-linkml/examples/README.md @@ -0,0 +1,5 @@ +# Examples of use of nwb_schema_language + +This folder contains example data conforming to nwb_schema_language + +The source for these is in [src/data](../src/data/examples) diff --git a/nwb-schema-linkml/mkdocs.yml b/nwb-schema-linkml/mkdocs.yml new file mode 100644 index 0000000..6f83531 --- /dev/null +++ b/nwb-schema-linkml/mkdocs.yml @@ -0,0 +1,25 @@ +--- +site_name: "nwb-schema-language" +theme: + name: material + # palette: + # scheme: slate + # primary: cyan + features: + - content.tabs.link +plugins: + - search + - mermaid2 +nav: + # - Home: home.md + - Index: index.md + - About: about.md +site_url: https://p2p_ld.github.io/nwb-schema-language +repo_url: https://github.com/p2p_ld/nwb-schema-language + +# Uncomment this block to enable use of Google Analytics. +# Replace the property value with your own ID. +# extra: +# analytics: +# provider: google +# property: G-XXXXXXXXXX diff --git a/nwb-schema-linkml/poetry.lock b/nwb-schema-linkml/poetry.lock new file mode 100644 index 0000000..fb27591 --- /dev/null +++ b/nwb-schema-linkml/poetry.lock @@ -0,0 +1,2521 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.5.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.7" +files = [ + {file = 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linkml:String . + +famrel:02 a owl:Class, + my_datamodel:FamilialRelationshipType ; + rdfs:label "PARENT_OF" . + +PATO:0001421 a owl:Class, + my_datamodel:PersonStatus ; + rdfs:label "ALIVE" . + +PATO:0001422 a owl:Class, + my_datamodel:PersonStatus ; + rdfs:label "DEAD" . + +schema:birthDate a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "birth_date" ; + rdfs:range linkml:String ; + skos:exactMatch schema:birthDate . + +schema:description a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "description" ; + rdfs:range linkml:String ; + skos:exactMatch schema:description . + +schema:email a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "primary_email" ; + rdfs:range linkml:String ; + skos:exactMatch schema:email . + +schema:identifier a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "id" ; + rdfs:range linkml:String ; + skos:exactMatch schema:identifier . + +schema:image a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "image" ; + rdfs:range linkml:String ; + skos:exactMatch schema:image . + +schema:name a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "name" ; + rdfs:range linkml:String ; + skos:exactMatch schema:name . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ended_at_time" ; + rdfs:range linkml:Date ; + skos:exactMatch . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "started_at_time" ; + rdfs:range linkml:Date ; + skos:exactMatch . + +my_datamodel:FamilialRelationship a owl:Class, + linkml:ClassDefinition ; + rdfs:label "FamilialRelationship" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass my_datamodel:FamilialRelationshipType ; + owl:onProperty my_datamodel:type ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass my_datamodel:Person ; + owl:onProperty my_datamodel:related_to ; + owl:qualifiedCardinality 1 ], + my_datamodel:Relationship . + + a owl:Class, + my_datamodel:PersonStatus ; + rdfs:label "UNKNOWN" . + +my_datamodel:Relationship a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Relationship" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:related_to ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:type ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty ] . + +my_datamodel:related_to a owl:ObjectProperty, + linkml:SlotDefinition . + +my_datamodel:type a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "type" ; + rdfs:range linkml:String . + +famrel:01 a owl:Class, + my_datamodel:FamilialRelationshipType ; + rdfs:label "CHILD_OF", + "SIBLING_OF" . + +my_datamodel:Address a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Address" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:city ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:street ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:postal_code ] ; + skos:exactMatch schema:PostalAddress . + +my_datamodel:FamilialRelationshipType a owl:Class, + linkml:EnumDefinition ; + rdfs:label "FamilialRelationshipType" ; + owl:unionOf ( famrel:01 famrel:02 famrel:01 ) ; + linkml:permissible_values famrel:01, + famrel:02 . + +my_datamodel:HasAliases a owl:Class, + linkml:ClassDefinition ; + rdfs:label "HasAliases" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty my_datamodel:aliases ], + linkml:mixin ; + skos:definition "A mixin applied to any class that can have aliases/alternateNames" . + +my_datamodel:NamedThing a owl:Class, + linkml:ClassDefinition ; + rdfs:label "NamedThing" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty schema:description ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty schema:name ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty schema:image ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty schema:identifier ; + owl:qualifiedCardinality 1 ] ; + skos:closeMatch schema:Thing ; + skos:definition "A generic grouping for any identifiable entity" . + +my_datamodel:Organization a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Organization" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:mission_statement ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty my_datamodel:founding_date ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty my_datamodel:aliases ], + my_datamodel:HasAliases, + my_datamodel:NamedThing ; + skos:definition "An organization such as a company or university" ; + skos:exactMatch schema:Organization . + +my_datamodel:Person a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Person" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty my_datamodel:aliases ], + [ a owl:Restriction ; + owl:allValuesFrom my_datamodel:FamilialRelationship ; + owl:onProperty my_datamodel:has_familial_relationships ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty my_datamodel:age_in_years ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass my_datamodel:Address ; + owl:onProperty my_datamodel:current_address ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty schema:birthDate ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty schema:email ], + my_datamodel:HasAliases, + my_datamodel:NamedThing ; + skos:definition "A person (alive, dead, undead, or fictional)." ; + skos:exactMatch schema:Person . + +my_datamodel:PersonStatus a owl:Class, + linkml:EnumDefinition ; + rdfs:label "PersonStatus" ; + owl:unionOf ( PATO:0001421 PATO:0001422 ) ; + linkml:permissible_values PATO:0001421, + PATO:0001422, + . + +my_datamodel:aliases a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "aliases" ; + rdfs:range linkml:String ; + skos:exactMatch schema:alternateName . + +linkml:ClassDefinition a owl:Class ; + rdfs:label "class_definition" . + +linkml:SlotDefinition a owl:Class ; + rdfs:label "slot_definition" . diff --git a/nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml b/nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml new file mode 100644 index 0000000..5dd8085 --- /dev/null +++ b/nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml @@ -0,0 +1,11 @@ +{ + "PATO": "http://purl.obolibrary.org/obo/PATO_", + "biolink": "https://w3id.org/biolink/", + "example": "https://example.org/", + "linkml": "https://w3id.org/linkml/", + "nwb_schema_language": "https://w3id.org/p2p_ld/nwb-schema-language/", + "schema": "http://schema.org/", + "NamedThing": { + "@id": "schema:Thing" + } +} diff --git a/nwb-schema-linkml/project/protobuf/nwb_schema_language.proto b/nwb-schema-linkml/project/protobuf/nwb_schema_language.proto new file mode 100644 index 0000000..d9c8412 --- /dev/null +++ b/nwb-schema-linkml/project/protobuf/nwb_schema_language.proto @@ -0,0 +1,23 @@ +// A generic grouping for any identifiable entity +message NamedThing + { + uriorcurie id = 0 + string name = 0 + string description = 0 + } +// Represents a Namespaces +message Namespaces + { + uriorcurie id = 0 + string name = 0 + string description = 0 + string primaryEmail = 0 + date birthDate = 0 + integer ageInYears = 0 + personStatus vitalStatus = 0 + } +// A holder for Namespaces objects +message NamespacesCollection + { + repeated namespaces entries = 0 + } diff --git a/nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl b/nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl new file mode 100644 index 0000000..9af53eb --- /dev/null +++ b/nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl @@ -0,0 +1,164 @@ +@prefix famrel: . +@prefix my_datamodel: . +@prefix rdf: . +@prefix schema: . +@prefix sh: . +@prefix xsd: . + +my_datamodel:HasAliases a sh:NodeShape ; + sh:closed true ; + sh:description "A mixin applied to any class that can have aliases/alternateNames" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:order 0 ; + sh:path my_datamodel:aliases ] ; + sh:targetClass my_datamodel:HasAliases . + +my_datamodel:NamedThing a sh:NodeShape ; + sh:closed true ; + sh:description "A generic grouping for any identifiable entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 0 ; + sh:path schema:identifier ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:name ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path schema:image ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path schema:description ] ; + sh:targetClass my_datamodel:NamedThing . + +my_datamodel:Registry a sh:NodeShape ; + sh:closed true ; + sh:description "Top level data container" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class schema:Person ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path my_datamodel:persons ], + [ sh:class schema:Organization ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path my_datamodel:organizations ] ; + sh:targetClass my_datamodel:Registry . + +my_datamodel:Relationship a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 0 ; + sh:path ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path my_datamodel:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path my_datamodel:related_to ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path ] ; + sh:targetClass my_datamodel:Relationship . + +schema:Organization a sh:NodeShape ; + sh:closed true ; + sh:description "An organization such as a company or university" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 1 ; + sh:path my_datamodel:founding_date ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path schema:description ], + [ sh:order 2 ; + sh:path my_datamodel:aliases ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path schema:image ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path my_datamodel:mission_statement ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path schema:identifier ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path schema:name ] ; + sh:targetClass schema:Organization . + +schema:Person a sh:NodeShape ; + sh:closed true ; + sh:description "A person (alive, dead, undead, or fictional)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 6 ; + sh:path schema:identifier ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path schema:description ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path schema:image ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path schema:email ; + sh:pattern "^\\S+@[\\S+\\.]+\\S+" ], + [ sh:maxCount 1 ; + sh:maxInclusive 999 ; + sh:minInclusive 0 ; + sh:order 2 ; + sh:path my_datamodel:age_in_years ], + [ sh:class schema:PostalAddress ; + sh:description "The address at which a person currently lives" ; + sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path my_datamodel:current_address ], + [ sh:class my_datamodel:FamilialRelationship ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path my_datamodel:has_familial_relationships ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:birthDate ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path schema:name ], + [ sh:order 5 ; + sh:path my_datamodel:aliases ] ; + sh:targetClass schema:Person . + +schema:PostalAddress a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 1 ; + sh:path my_datamodel:city ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path my_datamodel:postal_code ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path my_datamodel:street ] ; + sh:targetClass schema:PostalAddress . + +my_datamodel:FamilialRelationship a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 1 ; + sh:path ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path ], + [ sh:in ( famrel:01 famrel:02 famrel:01 ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path my_datamodel:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path my_datamodel:related_to ] ; + sh:targetClass my_datamodel:FamilialRelationship . diff --git a/nwb-schema-linkml/project/shex/nwb_schema_language.shex b/nwb-schema-linkml/project/shex/nwb_schema_language.shex new file mode 100644 index 0000000..5dc310e --- /dev/null +++ b/nwb-schema-linkml/project/shex/nwb_schema_language.shex @@ -0,0 +1,74 @@ +BASE +PREFIX rdf: +PREFIX xsd: +PREFIX linkml: +PREFIX schema1: + + +linkml:String xsd:string + +linkml:Integer xsd:integer + +linkml:Boolean xsd:boolean + +linkml:Float xsd:float + +linkml:Double xsd:double + +linkml:Decimal xsd:decimal + +linkml:Time xsd:time + +linkml:Date xsd:date + +linkml:Datetime xsd:dateTime + +linkml:DateOrDatetime linkml:DateOrDatetime + +linkml:Uriorcurie IRI + +linkml:Curie xsd:string + +linkml:Uri IRI + +linkml:Ncname xsd:string + +linkml:Objectidentifier IRI + +linkml:Nodeidentifier NONLITERAL + +linkml:Jsonpointer xsd:string + +linkml:Jsonpath xsd:string + +linkml:Sparqlpath xsd:string + + ( + CLOSED { + ( $ ( schema1:name @linkml:String ? ; + schema1:description @linkml:String ? + ) ; + rdf:type [ schema1:Thing ] + ) + } OR @ +) + + CLOSED { + ( $ ( & ; + rdf:type [ schema1:Thing ] ? ; + schema1:email @linkml:String ? ; + schema1:birthDate @linkml:Date ? ; + @linkml:Integer ? ; + @ ? + ) ; + rdf:type [ ] + ) +} + + CLOSED { + ( $ @ * ; + rdf:type [ ] ? + ) +} + + diff --git a/nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql b/nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql new file mode 100644 index 0000000..c21e019 --- /dev/null +++ b/nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql @@ -0,0 +1,24 @@ + + +CREATE TABLE "NamedThing" ( + id TEXT NOT NULL, + name TEXT, + description TEXT, + PRIMARY KEY (id) +); + +CREATE TABLE "Namespaces" ( + id TEXT NOT NULL, + name TEXT, + description TEXT, + primary_email TEXT, + birth_date DATE, + age_in_years INTEGER, + vital_status VARCHAR(7), + PRIMARY KEY (id) +); + +CREATE TABLE "NamespacesCollection" ( + entries TEXT, + PRIMARY KEY (entries) +); diff --git a/nwb-schema-linkml/pyproject.toml b/nwb-schema-linkml/pyproject.toml new file mode 100644 index 0000000..e8b9528 --- /dev/null +++ b/nwb-schema-linkml/pyproject.toml @@ -0,0 +1,30 @@ +[tool.poetry] +name = "nwb_schema_linkml" +version = "0.1.0" +description = "Translation of the nwb-schema-language to LinkML" +authors = ["Jonny Saunders "] +license = "GNU GPL v3.0" +readme = "README.md" +include = ["README.md", "src/nwb_schema_language/schema", "project"] + +[tool.poetry.dependencies] +python = "^3.9" +linkml-runtime = "^1.1.24" + +[tool.poetry-dynamic-versioning] +enable = true +vcs = "git" +style = "pep440" + +[tool.poetry.dev-dependencies] +linkml = "^1.3.5" +mkdocs-material = "^8.2.8" +mkdocs-mermaid2-plugin = "^0.6.0" +schemasheets = "^0.1.14" + +[build-system] +requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] +build-backend = "poetry_dynamic_versioning.backend" + +[tool.poetry.extras] +docs = ["linkml", "mkdocs-material"] \ No newline at end of file diff --git a/nwb-schema-linkml/src/data/examples/Namespaces-001.yaml b/nwb-schema-linkml/src/data/examples/Namespaces-001.yaml new file mode 100644 index 0000000..2f8802f --- /dev/null +++ b/nwb-schema-linkml/src/data/examples/Namespaces-001.yaml @@ -0,0 +1,7 @@ +# Example data object +--- +entries: + - id: example:Namespaces001 + name: foo bar + primary_email: foo.bar@example.com + age_in_years: 33 diff --git a/nwb-schema-linkml/src/docs/about.md b/nwb-schema-linkml/src/docs/about.md new file mode 100644 index 0000000..c326513 --- /dev/null +++ b/nwb-schema-linkml/src/docs/about.md @@ -0,0 +1,3 @@ +# nwb-schema-language + +Translation of the nwb-schema-language to LinkML diff --git a/nwb-schema-linkml/src/nwb_schema_language/_version.py b/nwb-schema-linkml/src/nwb_schema_language/_version.py new file mode 100644 index 0000000..7edc9ee --- /dev/null +++ b/nwb-schema-linkml/src/nwb_schema_language/_version.py @@ -0,0 +1,7 @@ +from importlib.metadata import version, PackageNotFoundError + +try: + __version__ = version(__name__) +except PackageNotFoundError: + # package not installed + __version__ = "0.0.0" diff --git a/nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py b/nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py new file mode 100644 index 0000000..6d64f5c --- /dev/null +++ b/nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py @@ -0,0 +1 @@ +from .nwb_schema_language import * diff --git a/nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py b/nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py new file mode 100644 index 0000000..c8a0c8d --- /dev/null +++ b/nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py @@ -0,0 +1,193 @@ +# Auto generated from nwb_schema_language.yaml by pythongen.py version: 0.0.1 +# Generation date: 2023-08-16T15:57:41 +# Schema: nwb-schema-language +# +# id: https://w3id.org/p2p_ld/nwb-schema-language +# description: Translation of the nwb-schema-language to LinkML +# license: GNU GPL v3.0 + +import dataclasses +import re +from jsonasobj2 import JsonObj, as_dict +from typing import Optional, List, Union, Dict, ClassVar, Any +from dataclasses import dataclass +from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions + +from linkml_runtime.utils.slot import Slot +from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode +from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int +from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs +from linkml_runtime.utils.formatutils import camelcase, underscore, sfx +from linkml_runtime.utils.enumerations import EnumDefinitionImpl +from rdflib import Namespace, URIRef +from linkml_runtime.utils.curienamespace import CurieNamespace +from linkml_runtime.linkml_model.types import Date, Integer, String, Uriorcurie +from linkml_runtime.utils.metamodelcore import URIorCURIE, XSDDate + +metamodel_version = "1.7.0" +version = None + +# Overwrite dataclasses _init_fn to add **kwargs in __init__ +dataclasses._init_fn = dataclasses_init_fn_with_kwargs + +# Namespaces +PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_') +BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/') +EXAMPLE = CurieNamespace('example', 'https://example.org/') +LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') +NWB_SCHEMA_LANGUAGE = CurieNamespace('nwb_schema_language', 'https://w3id.org/p2p_ld/nwb-schema-language/') +SCHEMA = CurieNamespace('schema', 'http://schema.org/') +DEFAULT_ = NWB_SCHEMA_LANGUAGE + + +# Types + +# Class references +class NamedThingId(URIorCURIE): + pass + + +class NamespacesId(NamedThingId): + pass + + +@dataclass +class NamedThing(YAMLRoot): + """ + A generic grouping for any identifiable entity + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = SCHEMA.Thing + class_class_curie: ClassVar[str] = "schema:Thing" + class_name: ClassVar[str] = "NamedThing" + class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.NamedThing + + id: Union[str, NamedThingId] = None + name: Optional[str] = None + description: Optional[str] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, NamedThingId): + self.id = NamedThingId(self.id) + + if self.name is not None and not isinstance(self.name, str): + self.name = str(self.name) + + if self.description is not None and not isinstance(self.description, str): + self.description = str(self.description) + + super().__post_init__(**kwargs) + + +@dataclass +class Namespaces(NamedThing): + """ + Represents a Namespaces + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Namespaces + class_class_curie: ClassVar[str] = "nwb_schema_language:Namespaces" + class_name: ClassVar[str] = "Namespaces" + class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Namespaces + + id: Union[str, NamespacesId] = None + primary_email: Optional[str] = None + birth_date: Optional[Union[str, XSDDate]] = None + age_in_years: Optional[int] = None + vital_status: Optional[Union[str, "PersonStatus"]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, NamespacesId): + self.id = NamespacesId(self.id) + + if self.primary_email is not None and not isinstance(self.primary_email, str): + self.primary_email = str(self.primary_email) + + if self.birth_date is not None and not isinstance(self.birth_date, XSDDate): + self.birth_date = XSDDate(self.birth_date) + + if self.age_in_years is not None and not isinstance(self.age_in_years, int): + self.age_in_years = int(self.age_in_years) + + if self.vital_status is not None and not isinstance(self.vital_status, PersonStatus): + self.vital_status = PersonStatus(self.vital_status) + + super().__post_init__(**kwargs) + + +@dataclass +class NamespacesCollection(YAMLRoot): + """ + A holder for Namespaces objects + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.NamespacesCollection + class_class_curie: ClassVar[str] = "nwb_schema_language:NamespacesCollection" + class_name: ClassVar[str] = "NamespacesCollection" + class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.NamespacesCollection + + entries: Optional[Union[Dict[Union[str, NamespacesId], Union[dict, Namespaces]], List[Union[dict, Namespaces]]]] = empty_dict() + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + self._normalize_inlined_as_dict(slot_name="entries", slot_type=Namespaces, key_name="id", keyed=True) + + super().__post_init__(**kwargs) + + +# Enumerations +class PersonStatus(EnumDefinitionImpl): + + ALIVE = PermissibleValue( + text="ALIVE", + description="the person is living", + meaning=PATO["0001421"]) + DEAD = PermissibleValue( + text="DEAD", + description="the person is deceased", + meaning=PATO["0001422"]) + UNKNOWN = PermissibleValue( + text="UNKNOWN", + description="the vital status is not known") + + _defn = EnumDefinition( + name="PersonStatus", + ) + +# Slots +class slots: + pass + +slots.id = Slot(uri=SCHEMA.identifier, name="id", curie=SCHEMA.curie('identifier'), + model_uri=NWB_SCHEMA_LANGUAGE.id, domain=None, range=URIRef) + +slots.name = Slot(uri=SCHEMA.name, name="name", curie=SCHEMA.curie('name'), + model_uri=NWB_SCHEMA_LANGUAGE.name, domain=None, range=Optional[str]) + +slots.description = Slot(uri=SCHEMA.description, name="description", curie=SCHEMA.curie('description'), + model_uri=NWB_SCHEMA_LANGUAGE.description, domain=None, range=Optional[str]) + +slots.primary_email = Slot(uri=SCHEMA.email, name="primary_email", curie=SCHEMA.curie('email'), + model_uri=NWB_SCHEMA_LANGUAGE.primary_email, domain=None, range=Optional[str]) + +slots.birth_date = Slot(uri=SCHEMA.birthDate, name="birth_date", curie=SCHEMA.curie('birthDate'), + model_uri=NWB_SCHEMA_LANGUAGE.birth_date, domain=None, range=Optional[Union[str, XSDDate]]) + +slots.age_in_years = Slot(uri=NWB_SCHEMA_LANGUAGE.age_in_years, name="age_in_years", curie=NWB_SCHEMA_LANGUAGE.curie('age_in_years'), + model_uri=NWB_SCHEMA_LANGUAGE.age_in_years, domain=None, range=Optional[int]) + +slots.vital_status = Slot(uri=NWB_SCHEMA_LANGUAGE.vital_status, name="vital_status", curie=NWB_SCHEMA_LANGUAGE.curie('vital_status'), + model_uri=NWB_SCHEMA_LANGUAGE.vital_status, domain=None, range=Optional[Union[str, "PersonStatus"]]) + +slots.namespacesCollection__entries = Slot(uri=NWB_SCHEMA_LANGUAGE.entries, name="namespacesCollection__entries", curie=NWB_SCHEMA_LANGUAGE.curie('entries'), + model_uri=NWB_SCHEMA_LANGUAGE.namespacesCollection__entries, domain=None, range=Optional[Union[Dict[Union[str, NamespacesId], Union[dict, Namespaces]], List[Union[dict, Namespaces]]]]) + +slots.Namespaces_primary_email = Slot(uri=SCHEMA.email, name="Namespaces_primary_email", curie=SCHEMA.curie('email'), + model_uri=NWB_SCHEMA_LANGUAGE.Namespaces_primary_email, domain=Namespaces, range=Optional[str], + pattern=re.compile(r'^\S+@[\S+\.]+\S+')) \ No newline at end of file diff --git a/nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml b/nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml new file mode 100644 index 0000000..0ce05e8 --- /dev/null +++ b/nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml @@ -0,0 +1,96 @@ +--- +id: https://w3id.org/p2p_ld/nwb-schema-language +name: nwb-schema-language +title: nwb-schema-language +description: |- + Translation of the nwb-schema-language to LinkML +license: GNU GPL v3.0 +see_also: + - https://p2p_ld.github.io/nwb-schema-language + +prefixes: + nwb_schema_language: https://w3id.org/p2p_ld/nwb-schema-language/ + linkml: https://w3id.org/linkml/ + biolink: https://w3id.org/biolink/ + schema: http://schema.org/ + PATO: http://purl.obolibrary.org/obo/PATO_ + example: https://example.org/ +default_prefix: nwb_schema_language +default_range: string + +imports: + - linkml:types + +classes: + + NamedThing: + description: >- + A generic grouping for any identifiable entity + slots: + - id + - name + - description + class_uri: schema:Thing + + Namespaces: + is_a: NamedThing + description: >- + Represents a Namespaces + slots: + - primary_email + - birth_date + - age_in_years + - vital_status + slot_usage: + primary_email: + pattern: "^\\S+@[\\S+\\.]+\\S+" + + NamespacesCollection: + tree_root: true + description: >- + A holder for Namespaces objects + attributes: + entries: + range: Namespaces + multivalued: true + inlined: true + +slots: + id: + identifier: true + slot_uri: schema:identifier + range: uriorcurie + description: A unique identifier for a thing + name: + slot_uri: schema:name + description: A human-readable name for a thing + description: + slot_uri: schema:description + description: A human-readable description for a thing + primary_email: + slot_uri: schema:email + description: The main email address of a person + birth_date: + slot_uri: schema:birthDate + range: date + description: Date on which a person is born + age_in_years: + range: integer + description: Number of years since birth + vital_status: + range: PersonStatus + description: living or dead status + +enums: + PersonStatus: + permissible_values: + ALIVE: + description: the person is living + meaning: PATO:0001421 + DEAD: + description: the person is deceased + meaning: PATO:0001422 + UNKNOWN: + description: the vital status is not known + todos: + - map this to an ontology diff --git a/nwb-schema-linkml/tests/__init__.py b/nwb-schema-linkml/tests/__init__.py new file mode 100644 index 0000000..158c731 --- /dev/null +++ b/nwb-schema-linkml/tests/__init__.py @@ -0,0 +1 @@ +"""Tests for nwb-schema-language.""" diff --git a/nwb-schema-linkml/tests/test_data.py b/nwb-schema-linkml/tests/test_data.py new file mode 100644 index 0000000..2e6a9a1 --- /dev/null +++ b/nwb-schema-linkml/tests/test_data.py @@ -0,0 +1,22 @@ +"""Data test.""" +import os +import glob +import unittest + +from linkml_runtime.loaders import yaml_loader +from nwb_schema_language.datamodel.nwb_schema_language import Namespaces + +ROOT = os.path.join(os.path.dirname(__file__), '..') +DATA_DIR = os.path.join(ROOT, "src", "data", "examples") + +EXAMPLE_FILES = glob.glob(os.path.join(DATA_DIR, '*.yaml')) + + +class TestData(unittest.TestCase): + """Test data and datamodel.""" + + def test_data(self): + """Date test.""" + for path in EXAMPLE_FILES: + obj = yaml_loader.load(path, target_class=Namespaces) + assert obj diff --git a/nwb-schema-linkml/utils/get-value.sh b/nwb-schema-linkml/utils/get-value.sh new file mode 100644 index 0000000..88f3b67 --- /dev/null +++ b/nwb-schema-linkml/utils/get-value.sh @@ -0,0 +1,4 @@ +#!/bin/bash +# get the value of a key in the about.yaml file +# https://stackoverflow.com/questions/1221833/pipe-output-and-capture-exit-status-in-bash +grep "^$1:" about.yaml | sed "s/$1:[[:space:]]//" ; test "${PIPESTATUS[0]}" -eq 0