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make linkml cookiecutter

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{
"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 <j@nny.fyi>",
"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
}

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---
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
...

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# 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

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---
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 }}

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/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/

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# 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/

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# 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)
<a id="code-of-conduct"></a>
## 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).
<a id="contributions"></a>
## Guidelines for Contributions and Requests
<a id="reporting-bugs"></a>
### Reporting problems with the data model
Please use our [Issue Tracker][issues] to report problems with the ontology.
<a id="requesting-terms"></a>
### Requesting new terms
Please use our [Issue Tracker][issues] to request a new term for the ontology.
<a id="adding-terms"></a>
### Adding new terms yourself
Please submit a [Pull Request][pulls] to submit a new term for consideration.
<a id="best-practices"></a>
## Best Practices
<a id="great-issues"></a>
### How to write a great issue
Please review GitHub's overview article,
["Tracking Your Work with Issues"][about-issues].
<a id="great-pulls"></a>
### 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/

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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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The licenses for most software and other practical works are designed
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Also add information on how to contact you by electronic and paper mail.
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This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
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You should also get your employer (if you work as a programmer) or school,
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For more information on this, and how to apply and follow the GNU GPL, see
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The GNU General Public License does not permit incorporating your program
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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

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# 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
<details>
Use the `make` command to generate project artefacts:
* `make all`: make everything
* `make deploy`: deploys site
</details>
## Credits
This project was made with
[linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).

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nwb-schema-linkml/about.yaml Normal file
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---
name: nwb_schema_language
author: Jonny Saunders <j@nny.fyi>
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

8
nwb-schema-linkml/config.env Normal file
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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

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nwb-schema-linkml/config.yaml Normal file
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# 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
...

7
nwb-schema-linkml/examples/Namespaces-001.yaml Normal file
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# Example data object
---
entries:
- id: example:Namespaces001
name: foo bar
primary_email: foo.bar@example.com
age_in_years: 33

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nwb-schema-linkml/examples/README.md Normal file
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# 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)

25
nwb-schema-linkml/mkdocs.yml Normal file
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---
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

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1
nwb-schema-linkml/project.Makefile Normal file
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## Add your own custom Makefile targets here

BIN
nwb-schema-linkml/project/excel/nwb_schema_language.xlsx Normal file
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Binary file not shown.

23
nwb-schema-linkml/project/graphql/nwb_schema_language.graphql Normal file
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@ -0,0 +1,23 @@
type NamedThing
{
id: Uriorcurie!
name: String
description: String
}
type Namespaces
{
id: Uriorcurie!
name: String
description: String
primaryEmail: String
birthDate: Date
ageInYears: Integer
vitalStatus: PersonStatus
}
type NamespacesCollection
{
entries: [Namespaces]
}

51
nwb-schema-linkml/project/jsonld/nwb_schema_language.context.jsonld Normal file
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@ -0,0 +1,51 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2023-08-16T15:57:40",
"source": "nwb_schema_language.yaml"
},
"@context": {
"PATO": {
"@id": "http://purl.obolibrary.org/obo/PATO_",
"@prefix": true
},
"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/",
"skos": "http://www.w3.org/2004/02/skos/core#",
"@vocab": "https://w3id.org/p2p_ld/nwb-schema-language/",
"age_in_years": {
"@type": "xsd:integer"
},
"birth_date": {
"@type": "xsd:date",
"@id": "schema:birthDate"
},
"description": {
"@id": "schema:description"
},
"id": "@id",
"name": {
"@id": "schema:name"
},
"entries": {
"@type": "@id"
},
"primary_email": {
"@id": "schema:email"
},
"vital_status": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
}
},
"NamedThing": {
"@id": "schema:Thing"
}
}
}

543
nwb-schema-linkml/project/jsonld/nwb_schema_language.jsonld Normal file
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{
"name": "nwb-schema-language",
"description": "Translation of the nwb-schema-language to LinkML",
"title": "nwb-schema-language",
"see_also": [
"https://p2p_ld.github.io/nwb-schema-language"
],
"id": "https://w3id.org/p2p_ld/nwb-schema-language",
"imports": [
"linkml:types"
],
"license": "GNU GPL v3.0",
"prefixes": [
{
"prefix_prefix": "nwb_schema_language",
"prefix_reference": "https://w3id.org/p2p_ld/nwb-schema-language/"
},
{
"prefix_prefix": "linkml",
"prefix_reference": "https://w3id.org/linkml/"
},
{
"prefix_prefix": "biolink",
"prefix_reference": "https://w3id.org/biolink/"
},
{
"prefix_prefix": "schema",
"prefix_reference": "http://schema.org/"
},
{
"prefix_prefix": "PATO",
"prefix_reference": "http://purl.obolibrary.org/obo/PATO_"
},
{
"prefix_prefix": "example",
"prefix_reference": "https://example.org/"
}
],
"default_prefix": "nwb_schema_language",
"default_range": "string",
"types": [
{
"name": "string",
"definition_uri": "https://w3id.org/linkml/String",
"description": "A character string",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Text"
],
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"@type": "TypeDefinition"
},
{
"name": "integer",
"definition_uri": "https://w3id.org/linkml/Integer",
"description": "An integer",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Integer"
],
"base": "int",
"uri": "http://www.w3.org/2001/XMLSchema#integer",
"@type": "TypeDefinition"
},
{
"name": "boolean",
"definition_uri": "https://w3id.org/linkml/Boolean",
"description": "A binary (true or false) value",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Boolean"
],
"base": "Bool",
"uri": "http://www.w3.org/2001/XMLSchema#boolean",
"repr": "bool",
"@type": "TypeDefinition"
},
{
"name": "float",
"definition_uri": "https://w3id.org/linkml/Float",
"description": "A real number that conforms to the xsd:float specification",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Float"
],
"base": "float",
"uri": "http://www.w3.org/2001/XMLSchema#float",
"@type": "TypeDefinition"
},
{
"name": "double",
"definition_uri": "https://w3id.org/linkml/Double",
"description": "A real number that conforms to the xsd:double specification",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"close_mappings": [
"schema:Float"
],
"base": "float",
"uri": "http://www.w3.org/2001/XMLSchema#double",
"@type": "TypeDefinition"
},
{
"name": "decimal",
"definition_uri": "https://w3id.org/linkml/Decimal",
"description": "A real number with arbitrary precision that conforms to the xsd:decimal specification",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"broad_mappings": [
"schema:Number"
],
"base": "Decimal",
"uri": "http://www.w3.org/2001/XMLSchema#decimal",
"@type": "TypeDefinition"
},
{
"name": "time",
"definition_uri": "https://w3id.org/linkml/Time",
"description": "A time object represents a (local) time of day, independent of any particular day",
"notes": [
"URI is dateTime because OWL reasoners do not work with straight date or time"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Time"
],
"base": "XSDTime",
"uri": "http://www.w3.org/2001/XMLSchema#time",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "date",
"definition_uri": "https://w3id.org/linkml/Date",
"description": "a date (year, month and day) in an idealized calendar",
"notes": [
"URI is dateTime because OWL reasoners don't work with straight date or time"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Date"
],
"base": "XSDDate",
"uri": "http://www.w3.org/2001/XMLSchema#date",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "datetime",
"definition_uri": "https://w3id.org/linkml/Datetime",
"description": "The combination of a date and time",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:DateTime"
],
"base": "XSDDateTime",
"uri": "http://www.w3.org/2001/XMLSchema#dateTime",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "date_or_datetime",
"definition_uri": "https://w3id.org/linkml/DateOrDatetime",
"description": "Either a date or a datetime",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "https://w3id.org/linkml/DateOrDatetime",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "uriorcurie",
"definition_uri": "https://w3id.org/linkml/Uriorcurie",
"description": "a URI or a CURIE",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "URIorCURIE",
"uri": "http://www.w3.org/2001/XMLSchema#anyURI",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "curie",
"definition_uri": "https://w3id.org/linkml/Curie",
"conforms_to": "https://www.w3.org/TR/curie/",
"description": "a compact URI",
"comments": [
"in RDF serializations this MUST be expanded to a URI",
"in non-RDF serializations MAY be serialized as the compact representation"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "Curie",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "uri",
"definition_uri": "https://w3id.org/linkml/Uri",
"conforms_to": "https://www.ietf.org/rfc/rfc3987.txt",
"description": "a complete URI",
"comments": [
"in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"close_mappings": [
"schema:URL"
],
"base": "URI",
"uri": "http://www.w3.org/2001/XMLSchema#anyURI",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "ncname",
"definition_uri": "https://w3id.org/linkml/Ncname",
"description": "Prefix part of CURIE",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "NCName",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "objectidentifier",
"definition_uri": "https://w3id.org/linkml/Objectidentifier",
"description": "A URI or CURIE that represents an object in the model.",
"comments": [
"Used for inheritance and type checking"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "ElementIdentifier",
"uri": "http://www.w3.org/ns/shex#iri",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "nodeidentifier",
"definition_uri": "https://w3id.org/linkml/Nodeidentifier",
"description": "A URI, CURIE or BNODE that represents a node in a model.",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "NodeIdentifier",
"uri": "http://www.w3.org/ns/shex#nonLiteral",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "jsonpointer",
"definition_uri": "https://w3id.org/linkml/Jsonpointer",
"conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901",
"description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "jsonpath",
"definition_uri": "https://w3id.org/linkml/Jsonpath",
"conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html",
"description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "sparqlpath",
"definition_uri": "https://w3id.org/linkml/Sparqlpath",
"conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths",
"description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.",
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
}
],
"enums": [
{
"name": "PersonStatus",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/PersonStatus",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"permissible_values": [
{
"text": "ALIVE",
"description": "the person is living",
"meaning": "PATO:0001421"
},
{
"text": "DEAD",
"description": "the person is deceased",
"meaning": "PATO:0001422"
},
{
"text": "UNKNOWN",
"description": "the vital status is not known",
"todos": [
"map this to an ontology"
]
}
]
}
],
"slots": [
{
"name": "id",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/id",
"description": "A unique identifier for a thing",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"http://schema.org/identifier"
],
"slot_uri": "http://schema.org/identifier",
"identifier": true,
"owner": "NamedThing",
"domain_of": [
"NamedThing"
],
"range": "uriorcurie",
"required": true,
"@type": "SlotDefinition"
},
{
"name": "name",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/name",
"description": "A human-readable name for a thing",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"http://schema.org/name"
],
"slot_uri": "http://schema.org/name",
"owner": "NamedThing",
"domain_of": [
"NamedThing"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "description",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/description",
"description": "A human-readable description for a thing",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"http://schema.org/description"
],
"slot_uri": "http://schema.org/description",
"owner": "NamedThing",
"domain_of": [
"NamedThing"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "primary_email",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/primary_email",
"description": "The main email address of a person",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"http://schema.org/email"
],
"slot_uri": "http://schema.org/email",
"owner": "Namespaces",
"domain_of": [
"Namespaces"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "birth_date",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/birth_date",
"description": "Date on which a person is born",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"http://schema.org/birthDate"
],
"slot_uri": "http://schema.org/birthDate",
"owner": "Namespaces",
"domain_of": [
"Namespaces"
],
"range": "date",
"@type": "SlotDefinition"
},
{
"name": "age_in_years",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/age_in_years",
"description": "Number of years since birth",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/age_in_years",
"owner": "Namespaces",
"domain_of": [
"Namespaces"
],
"range": "integer",
"@type": "SlotDefinition"
},
{
"name": "vital_status",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/vital_status",
"description": "living or dead status",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/vital_status",
"owner": "Namespaces",
"domain_of": [
"Namespaces"
],
"range": "PersonStatus",
"@type": "SlotDefinition"
},
{
"name": "namespacesCollection__entries",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/entries",
"multivalued": true,
"alias": "entries",
"owner": "NamespacesCollection",
"domain_of": [
"NamespacesCollection"
],
"range": "Namespaces",
"inlined": true,
"@type": "SlotDefinition"
},
{
"name": "Namespaces_primary_email",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/primary_email",
"description": "The main email address of a person",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"http://schema.org/email"
],
"is_a": "primary_email",
"domain": "Namespaces",
"slot_uri": "http://schema.org/email",
"alias": "primary_email",
"owner": "Namespaces",
"domain_of": [
"Namespaces"
],
"is_usage_slot": true,
"usage_slot_name": "primary_email",
"range": "string",
"pattern": "^\\S+@[\\S+\\.]+\\S+",
"@type": "SlotDefinition"
}
],
"classes": [
{
"name": "NamedThing",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/NamedThing",
"description": "A generic grouping for any identifiable entity",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"mappings": [
"schema:Thing"
],
"slots": [
"id",
"name",
"description"
],
"slot_usage": {},
"class_uri": "http://schema.org/Thing",
"@type": "ClassDefinition"
},
{
"name": "Namespaces",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Namespaces",
"description": "Represents a Namespaces",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"is_a": "NamedThing",
"slots": [
"id",
"name",
"description",
"Namespaces_primary_email",
"birth_date",
"age_in_years",
"vital_status"
],
"slot_usage": {},
"class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Namespaces",
"@type": "ClassDefinition"
},
{
"name": "NamespacesCollection",
"definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/NamespacesCollection",
"description": "A holder for Namespaces objects",
"from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
"slots": [
"namespacesCollection__entries"
],
"slot_usage": {},
"attributes": [
{
"name": "entries",
"multivalued": true,
"range": "Namespaces",
"inlined": true,
"@type": "SlotDefinition"
}
],
"class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/NamespacesCollection",
"tree_root": true,
"@type": "ClassDefinition"
}
],
"metamodel_version": "1.7.0",
"source_file": "nwb_schema_language.yaml",
"source_file_date": "2023-08-16T15:45:06",
"source_file_size": 2270,
"generation_date": "2023-08-16T15:57:40",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/nwb_schema_language.context.jsonld",
"https://w3id.org/linkml/types.context.jsonld",
{
"@base": "https://w3id.org/p2p_ld/nwb-schema-language/"
}
]
}

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{
"$defs": {
"NamedThing": {
"additionalProperties": false,
"description": "A generic grouping for any identifiable entity",
"properties": {
"description": {
"description": "A human-readable description for a thing",
"type": "string"
},
"id": {
"description": "A unique identifier for a thing",
"type": "string"
},
"name": {
"description": "A human-readable name for a thing",
"type": "string"
}
},
"required": [
"id"
],
"title": "NamedThing",
"type": "object"
},
"Namespaces": {
"additionalProperties": false,
"description": "Represents a Namespaces",
"properties": {
"age_in_years": {
"description": "Number of years since birth",
"type": "integer"
},
"birth_date": {
"description": "Date on which a person is born",
"format": "date",
"type": "string"
},
"description": {
"description": "A human-readable description for a thing",
"type": "string"
},
"id": {
"description": "A unique identifier for a thing",
"type": "string"
},
"name": {
"description": "A human-readable name for a thing",
"type": "string"
},
"primary_email": {
"description": "The main email address of a person",
"pattern": "^\\S+@[\\S+\\.]+\\S+",
"type": "string"
},
"vital_status": {
"$ref": "#/$defs/PersonStatus",
"description": "living or dead status"
}
},
"required": [
"id"
],
"title": "Namespaces",
"type": "object"
},
"NamespacesCollection": {
"additionalProperties": false,
"description": "A holder for Namespaces objects",
"properties": {
"entries": {
"additionalProperties": {
"anyOf": [
{
"$ref": "#/$defs/Namespaces__identifier_optional"
},
{
"type": "null"
}
]
},
"type": "object"
}
},
"title": "NamespacesCollection",
"type": "object"
},
"Namespaces__identifier_optional": {
"additionalProperties": false,
"description": "Represents a Namespaces",
"properties": {
"age_in_years": {
"description": "Number of years since birth",
"type": "integer"
},
"birth_date": {
"description": "Date on which a person is born",
"format": "date",
"type": "string"
},
"description": {
"description": "A human-readable description for a thing",
"type": "string"
},
"id": {
"description": "A unique identifier for a thing",
"type": "string"
},
"name": {
"description": "A human-readable name for a thing",
"type": "string"
},
"primary_email": {
"description": "The main email address of a person",
"pattern": "^\\S+@[\\S+\\.]+\\S+",
"type": "string"
},
"vital_status": {
"$ref": "#/$defs/PersonStatus",
"description": "living or dead status"
}
},
"required": [],
"title": "Namespaces",
"type": "object"
},
"PersonStatus": {
"description": "",
"enum": [
"ALIVE",
"DEAD",
"UNKNOWN"
],
"title": "PersonStatus",
"type": "string"
}
},
"$id": "https://w3id.org/p2p_ld/nwb-schema-language",
"$schema": "http://json-schema.org/draft-07/schema#",
"additionalProperties": true,
"description": "A holder for Namespaces objects",
"metamodel_version": "1.7.0",
"properties": {
"entries": {
"additionalProperties": {
"anyOf": [
{
"$ref": "#/$defs/Namespaces__identifier_optional"
},
{
"type": "null"
}
]
},
"type": "object"
}
},
"title": "nwb-schema-language",
"type": "object",
"version": null
}

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@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> .
@prefix PATO: <http://purl.obolibrary.org/obo/PATO_> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix famrel: <http://example.org/famrel/> .
@prefix linkml: <https://w3id.org/linkml/> .
@prefix my_datamodel: <https://w3id.org/my_org/my_datamodel> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <http://schema.org/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
linkml:SubsetDefinition a owl:Class ;
rdfs:label "subset_definition" .
linkml:TypeDefinition a owl:Class ;
rdfs:label "type_definition" .
linkml:topValue a owl:DatatypeProperty ;
rdfs:label "value" .
my_datamodel: a owl:Ontology ;
rdfs:label "my_datamodel" ;
IAO:0000700 my_datamodel:Address,
my_datamodel:HasAliases,
my_datamodel:NamedThing,
my_datamodel:Registry,
my_datamodel:Relationship ;
dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
dcterms:title "My Datamodel" ;
rdfs:seeAlso "https://example.org/" ;
linkml:generation_date "2022-09-06T10:01:46" ;
linkml:metamodel_version "1.7.0" ;
linkml:source_file "nwb_schema_language.yaml" ;
linkml:source_file_date "2022-09-06T10:00:58" ;
linkml:source_file_size 3771 .
my_datamodel:employed_at a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "employed_at" ;
rdfs:range my_datamodel:Organization .
my_datamodel:is_current a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "is_current" ;
rdfs:range linkml:Boolean .
my_datamodel:Registry a owl:Class,
linkml:ClassDefinition ;
rdfs:label "Registry" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:allValuesFrom my_datamodel:Person ;
owl:onProperty my_datamodel:persons ],
[ a owl:Restriction ;
owl:allValuesFrom my_datamodel:Organization ;
owl:onProperty my_datamodel:organizations ] ;
skos:definition "Top level data container" .
my_datamodel:age_in_years a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "age_in_years" ;
rdfs:range linkml:Integer .
my_datamodel:city a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "city" ;
rdfs:range linkml:String .
my_datamodel:current_address a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "current_address" ;
rdfs:range my_datamodel:Address ;
skos:definition "The address at which a person currently lives" .
my_datamodel:founding_date a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "founding_date" ;
rdfs:range linkml:String .
my_datamodel:has_familial_relationships a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "has_familial_relationships" ;
rdfs:range my_datamodel:FamilialRelationship .
my_datamodel:mission_statement a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "mission_statement" ;
rdfs:range linkml:String .
my_datamodel:organizations a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "organizations" ;
rdfs:range my_datamodel:Organization .
my_datamodel:persons a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "persons" ;
rdfs:range my_datamodel:Person .
my_datamodel:postal_code a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "postal_code" ;
rdfs:range linkml:String .
my_datamodel:street a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "street" ;
rdfs:range 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 .
<http://www.w3.org/ns/prov#endedAtTime> a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "ended_at_time" ;
rdfs:range linkml:Date ;
skos:exactMatch <http://www.w3.org/ns/prov#endedAtTime> .
<http://www.w3.org/ns/prov#startedAtTime> a owl:ObjectProperty,
linkml:SlotDefinition ;
rdfs:label "started_at_time" ;
rdfs:range linkml:Date ;
skos:exactMatch <http://www.w3.org/ns/prov#startedAtTime> .
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 .
<https://w3id.org/my_org/my_datamodelPersonStatus#UNKNOWN> 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 <http://www.w3.org/ns/prov#endedAtTime> ],
[ a owl:Restriction ;
owl:maxQualifiedCardinality 1 ;
owl:onClass linkml:Date ;
owl:onProperty <http://www.w3.org/ns/prov#startedAtTime> ] .
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 <https://w3id.org/my_org/my_datamodelPersonStatus#UNKNOWN> ) ;
linkml:permissible_values PATO:0001421,
PATO:0001422,
<https://w3id.org/my_org/my_datamodelPersonStatus#UNKNOWN> .
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" .

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{
"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"
}
}

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// 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
}

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@prefix famrel: <http://example.org/famrel/> .
@prefix my_datamodel: <https://w3id.org/my_org/my_datamodel> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix schema: <http://schema.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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 <http://www.w3.org/ns/prov#startedAtTime> ],
[ 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 <http://www.w3.org/ns/prov#endedAtTime> ] ;
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 <http://www.w3.org/ns/prov#endedAtTime> ],
[ sh:maxCount 1 ;
sh:order 0 ;
sh:path <http://www.w3.org/ns/prov#startedAtTime> ],
[ 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 .

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BASE <https://w3id.org/p2p_ld/nwb-schema-language/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX linkml: <https://w3id.org/linkml/>
PREFIX schema1: <http://schema.org/>
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
<NamedThing> (
CLOSED {
( $<NamedThing_tes> ( schema1:name @linkml:String ? ;
schema1:description @linkml:String ?
) ;
rdf:type [ schema1:Thing ]
)
} OR @<Namespaces>
)
<Namespaces> CLOSED {
( $<Namespaces_tes> ( &<NamedThing_tes> ;
rdf:type [ schema1:Thing ] ? ;
schema1:email @linkml:String ? ;
schema1:birthDate @linkml:Date ? ;
<age_in_years> @linkml:Integer ? ;
<vital_status> @<PersonStatus> ?
) ;
rdf:type [ <Namespaces> ]
)
}
<NamespacesCollection> CLOSED {
( $<NamespacesCollection_tes> <entries> @<Namespaces> * ;
rdf:type [ <NamespacesCollection> ] ?
)
}

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nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql Normal file
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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)
);

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nwb-schema-linkml/pyproject.toml Normal file
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[tool.poetry]
name = "nwb_schema_linkml"
version = "0.1.0"
description = "Translation of the nwb-schema-language to LinkML"
authors = ["Jonny Saunders <j@nny.fyi>"]
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"]

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nwb-schema-linkml/src/data/examples/Namespaces-001.yaml Normal file
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# Example data object
---
entries:
- id: example:Namespaces001
name: foo bar
primary_email: foo.bar@example.com
age_in_years: 33

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nwb-schema-linkml/src/docs/about.md Normal file
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# nwb-schema-language
Translation of the nwb-schema-language to LinkML

7
nwb-schema-linkml/src/nwb_schema_language/_version.py Normal file
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from importlib.metadata import version, PackageNotFoundError
try:
__version__ = version(__name__)
except PackageNotFoundError:
# package not installed
__version__ = "0.0.0"

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nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py Normal file
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from .nwb_schema_language import *

193
nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py Normal file
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# 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+'))

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nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml Normal file
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---
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

1
nwb-schema-linkml/tests/__init__.py Normal file
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"""Tests for nwb-schema-language."""

22
nwb-schema-linkml/tests/test_data.py Normal file
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"""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

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nwb-schema-linkml/utils/get-value.sh Normal file
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#!/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