From c743fd0b38d529290a1685da30ab99fe26741132 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 5 Mar 2024 18:41:32 -0800 Subject: [PATCH] metamodel docs (#133) * Adding metamodel docs * Adding docs target. Sphinx update * docs-target --- .github/workflows/doc_pages.yaml | 3 +- Makefile | 73 +-- docs/conf.py | 36 +- docs/index.rst | 1 + docs/metamodels/index.rst | 23 + poetry.lock | 961 ++++++++++++++----------------- pyproject.toml | 2 +- 7 files changed, 491 insertions(+), 608 deletions(-) create mode 100644 docs/metamodels/index.rst diff --git a/.github/workflows/doc_pages.yaml b/.github/workflows/doc_pages.yaml index a6a0669..510ecd4 100644 --- a/.github/workflows/doc_pages.yaml +++ b/.github/workflows/doc_pages.yaml @@ -27,6 +27,7 @@ jobs: run: | mkdir gh-pages touch gh-pages/.nojekyll + make all-docs cd docs/ poetry run sphinx-build -b html . _build cp -r _build/* ../gh-pages/ @@ -37,4 +38,4 @@ jobs: with: branch: gh-pages force: true - folder: gh-pages \ No newline at end of file + folder: gh-pages diff --git a/Makefile b/Makefile index 0e7e671..ad4a5a1 100644 --- a/Makefile +++ b/Makefile @@ -1,76 +1,39 @@ RUN = poetry run VERSION = $(shell git tag | tail -1) +MODELS = cadsr frictionless -.PHONY: all clean test +.PHONY: all clean test all-docs sphinx-html -all: clean test target/soil_meanings.yaml +all: clean test -clean: - rm -rf target/soil_meanings.yaml - rm -rf target/soil_meanings_generated.yaml - rm -rf target/availabilities_g_s_strain_202112151116.yaml - rm -rf target/availabilities_g_s_strain_202112151116_org_meanings.yaml - test: $(RUN) pytest tests/ schema_automator/metamodels/%.py: schema_automator/metamodels/%.yaml $(RUN) gen-python $< > $@.tmp && mv $@.tmp $@ -# tried to find a single meaning for each permissible value -# unlike term mapping, which can tolerate multiple mapped terms -target/soil_meanings.yaml: tests/resources/mixs/terms.yaml - poetry run enum_annotator \ - --modelfile $< \ - --requested_enum_name fao_class_enum \ - --ontology_string ENVO > $@ - -# validate that it's still valid LinkML -# FileNotFoundError: [Errno 2] No such file or directory: '/Users/MAM/Documents/gitrepos/linkml-model-enrichment/target/ranges.yaml' -# cp tests/resources/mixs/*yaml target -target/soil_meanings_generated.yaml: target/soil_meanings.yaml - poetry run gen-yaml $< > $@ - -# requires Felix files -# add demonstration SQL file -target/availabilities_g_s_strain_202112151116.yaml: local/availabilities_g_s_strain_202112151116.tsv - poetry run tsv2linkml \ - --enum-columns organism \ - --output $@ \ - --class_name availabilities \ - --schema_name availabilities $< - -# KeyError: 'iri' could mean that an unrecognized ontology name was used -target/availabilities_g_s_strain_202112151116_org_meanings.yaml: target/availabilities_g_s_strain_202112151116.yaml - poetry run enum_annotator \ - --modelfile $< \ - --requested_enum_name organism_enum \ - --ontology_string NCBITAXON > $@ - -target/availabilities_g_s_strain_202112151116_org_meanings_curateable.tsv: target/availabilities_g_s_strain_202112151116_org_meanings.yaml - poetry run enums_to_curateable \ - --modelfile $< \ - --enum organism_enum \ - --tsv_out $@ - -# do some curation on target/availabilities_g_s_strain_202112151116_org_meanings_curateable.tsv -# and save as target/availabilities_g_s_strain_202112151116_org_meanings_curated.txt -# Excel wants to call it "*.txt". I'm saving as UTF 16 so I can be sure about the encoding at import time. - -target/availabilities_g_s_strain_202112151116_org_meanings_curated.yaml: target/availabilities_g_s_strain_202112151116_org_meanings_curated.txt - poetry run curated_to_enums \ - --tsv_in $< \ - --tsv_encoding utf_16 \ - --model_in target/availabilities_g_s_strain_202112151116_org_meanings.yaml \ - --curated_yaml $@ \ - --selected_enum organism_enum # create a convenient wrapper script; # this can be used outside the poetry environment bin/schemauto: echo `poetry run which schemauto` '"$$@"' > $@ && chmod +x $@ +######################## +#### Metamodel docs #### +######################## + +all-docs: $(patsubst %,docs-%,$(MODELS)) + +docs-dosdp: schema_automator/metamodels/dosdp/dosdp_linkml.yaml + $(RUN) gen-doc -d docs/metamodels/dosdp $< + +docs-%: schema_automator/metamodels/%.yaml + $(RUN) gen-doc -d docs/metamodels/$* $< + +sphinx-%: + cd docs && $(RUN) make $* +.PHONY: sphinx-% ################################################ #### Commands for building the Docker image #### diff --git a/docs/conf.py b/docs/conf.py index b45bdcc..ac52fa6 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -33,32 +33,32 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.githubpages', - 'sphinx.ext.autosectionlabel', - 'sphinx_pdj_theme', - 'sphinx_click', - 'sphinx.ext.viewcode', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.autosummary', - 'myst_parser', - 'sphinx.ext.intersphinx', - 'sphinxcontrib.mermaid' + "sphinx.ext.autodoc", + "sphinx.ext.githubpages", + "sphinx.ext.autosectionlabel", + "sphinx_pdj_theme", + "sphinx_click", + "sphinx.ext.viewcode", + "sphinx.ext.todo", + "sphinx.ext.coverage", + "sphinx.ext.autosummary", + "myst_parser", + "sphinx.ext.intersphinx", + "sphinxcontrib.mermaid" ] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: -# source_suffix = ['.rst', '.md'] -source_suffix = ['.rst', '.md'] +# source_suffix = [".rst", ".md"] +source_suffix = [".rst", ".md"] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # -- Options for HTML output ------------------------------------------------- @@ -66,10 +66,10 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -#html_theme = 'sphinx_pdj_theme' +#html_theme = "sphinx_pdj_theme" #html_theme_path = [sphinx_pdj_theme.get_html_theme_path()] # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] diff --git a/docs/index.rst b/docs/index.rst index dfd4006..1c11982 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -28,6 +28,7 @@ schema frameworks, including: install cli packages/index + metamodels/index Indices and tables diff --git a/docs/metamodels/index.rst b/docs/metamodels/index.rst new file mode 100644 index 0000000..4df48cb --- /dev/null +++ b/docs/metamodels/index.rst @@ -0,0 +1,23 @@ +Source Metamodels +================= + +Schema Automator makes use of LinkML Schema representations of source +metamodels in order to define transformations. + +.. toctree:: + :maxdepth: 3 + :caption: Contents: + + index + cadsr/index + frictionless/index + dosdp/index + fhir/index + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/poetry.lock b/poetry.lock index eba0cac..34cffab 100644 --- a/poetry.lock +++ b/poetry.lock @@ -53,14 +53,14 @@ files = [ [[package]] name = "anyio" -version = "4.2.0" +version = "4.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "dev" optional = false python-versions = ">=3.8" files = [ - 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python-versions = "^3.9" -content-hash = "edb0658566f95ab75690a51a7abe039c30734f24cf81a5ab0e670d1693755be2" +content-hash = "14010772a2ea7449e1e46170106c1eeee97480d74b6a3897f8614d8e51e602e7" diff --git a/pyproject.toml b/pyproject.toml index 3f6a701..c20b7ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ pytest = ">=7.1.1" Sphinx = ">=4.4.0" sphinx-pdj-theme = ">=0.2.1" sphinx-click = ">=3.1.0" -sphinxcontrib-mermaid = ">=0.7.1" +sphinxcontrib-mermaid = ">=0.9.2" myst-parser = "*" jupyter = ">=1.0.0" lxml = ">=4.9.1"