Shex for Standard Annotations

.github/workflows/gen-project-linkml.yaml

@@ -22,10 +22,10 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v2
 
-      - name: Set up Python ${{ "{{" }} matrix.python-version {{ "}}" }}
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
-          python-version: ${{ "{{" }} matrix.python-version {{ "}}" }}
+          python-version: ${{ matrix.python-version }}
 
       #----------------------------------------------
       #          install & configure poetry

.vscode/launch.json

@@ -0,0 +1,16 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Python: Current File",
+      "type": "python",
+      "request": "launch",
+      "program": "${file}",
+      "console": "integratedTerminal",
+      "justMyCode": true
+    }
+  ]
+}

README.md

@@ -4,7 +4,6 @@
 
 Using RDF Shapes to define the schema of Gene Ontology Causal Activity Models
 
-
 # Schema
 
 See [shapes/go-cam-shapes.shex](shapes/go-cam-shapes.shex)

python/.gitignore

@@ -0,0 +1,138 @@
+# 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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

python/Makefile

@@ -42,16 +42,16 @@ f-%: tests/data/f-%.ttl
 	python ./gocam_validator.py $< && exit -1 || echo FAILED AS EXPECTED
 
 gen-python:
-	rm -f shex_json_linkml.py && gen-python schema/shex_json_linkml.yaml > shex_json_linkml.py
+	rm -f shex_json_linkml.py && gen-python schema/shex_term_metadata_json_linkml.yaml > shex_term_metadata_json_linkml.py
 
 #gen-pydantic:
 #	rm -f shex_json_linkml.py && gen-pydantic schema/shex_json_linkml.yaml > shex_json_linkml.py
 
 gen-jsonschema:
-	rm -f target/jsonschema/shex_json_linkml.json && gen-json-schema schema/shex_json_linkml.yaml > target/jsonschema/shex_json_linkml.json
+	rm -f target/jsonschema/shex_terms_metadata_json_linkml.json && gen-json-schema schema/shex_terms_metadata_json_linkml.yaml > target/jsonschema/shex_terms_metadata_json_linkml.json
 
 gen-typescript:
-	rm -f target/typescript/shex_json_linkml.ts && gen-typescript schema/shex_json_linkml.yaml > target/typescript/shex_json_linkml.ts
+	rm -f target/typescript/shex_terms_metadata_json_linkml.ts && gen-typescript schema/shex_terms_metadata_json_linkml.yaml > target/typescript/shex_terms_metadata_json_linkml.ts
 
 linkml: gen-python gen-jsonschema gen-typescript