From 52822bb0036d916a716680e2d5a3b049a068bb46 Mon Sep 17 00:00:00 2001 From: yelenacox Date: Fri, 26 Jun 2026 16:15:10 -0500 Subject: [PATCH 1/2] Modifying docs --- docs/schema/cam_source_enums.yaml | 19 +++++-- docs/term-expansion.md | 15 ++++++ mkdocs.yml | 85 ++++++++++++++++--------------- 3 files changed, 72 insertions(+), 47 deletions(-) create mode 100644 docs/term-expansion.md diff --git a/docs/schema/cam_source_enums.yaml b/docs/schema/cam_source_enums.yaml index 8234c29..61bd2cf 100644 --- a/docs/schema/cam_source_enums.yaml +++ b/docs/schema/cam_source_enums.yaml @@ -369,6 +369,8 @@ enums: relationship_types: - rdfs:subClassOf is_direct: false + include_self: false + traverse_up: false EnumDataUseModifier: name: EnumDataUseModifier definition_uri: https://includedcc.org/common-access-model/EnumDataUseModifier/EnumDataUseModifier @@ -382,6 +384,8 @@ enums: relationship_types: - rdfs:subClassOf is_direct: false + include_self: false + traverse_up: false EnumProgram: name: EnumProgram definition_uri: https://includedcc.org/common-access-model/EnumProgram/EnumProgram @@ -859,6 +863,8 @@ enums: relationship_types: - rdfs:subClassOf is_direct: false + include_self: true + traverse_up: false EnumLaterality: name: EnumLaterality definition_uri: https://includedcc.org/common-access-model/EnumLaterality/EnumLaterality @@ -876,7 +882,8 @@ enums: relationship_types: - rdfs:subClassOf is_direct: false - include_self: false + include_self: true + traverse_up: false EnumEDAMDataTypes: name: EnumEDAMDataTypes definition_uri: https://includedcc.org/common-access-model/EnumEDAMDataTypes/EnumEDAMDataTypes @@ -890,6 +897,7 @@ enums: - rdfs:subClassOf is_direct: false include_self: false + traverse_up: false EnumFileHashType: name: EnumFileHashType definition_uri: https://includedcc.org/common-access-model/EnumFileHashType/EnumFileHashType @@ -960,7 +968,8 @@ classes: RequiredClass: name: RequiredClass definition_uri: https://includedcc.org/common-access-model/RequiredClass - description: Required description for classes. + description: This is a placeholder class to satisfy the LinkML requirement of + at least one class and is not otherwise used. from_schema: https://includedcc.org/cam-source-enums exact_mappings: - cam:RequiredClass @@ -989,7 +998,7 @@ classes: class_uri: cam:RequiredClass metamodel_version: 1.11.0 source_file: cam_source_enums.yaml -source_file_date: '2026-05-20T09:58:28' -source_file_size: 2443 -generation_date: '2026-05-20T09:59:39' +source_file_date: '2026-06-26T16:03:28' +source_file_size: 2350 +generation_date: '2026-06-26T16:12:35' diff --git a/docs/term-expansion.md b/docs/term-expansion.md new file mode 100644 index 0000000..b974f61 --- /dev/null +++ b/docs/term-expansion.md @@ -0,0 +1,15 @@ +# Term expansion + +This is the source of the enumeration files to be materialized by the [Term-Weaver](https://github.com/include-dcc/term-weaver) tool. + +## [LinkML properties](https://linkml.io/linkml-model/latest/docs/ReachabilityQuery/) currently supported * +- source_ontology +- source_nodes +- relationship_types + - only supporting rdfs:subClassOf +- is_direct + - true/false +- include_self + - true/false + +* It does not currently support 'traverse_up' diff --git a/mkdocs.yml b/mkdocs.yml index 87d1822..90bec1f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,63 +1,64 @@ --- site_name: "cam-source-enums" theme: - # https://www.mkdocs.org/user-guide/configuration/#theme - name: material - icon: - logo: material/book-open-page-variant - # palette: - # scheme: slate - # primary: cyan - features: - - content.tabs.link - - header.autohide # maximum screen space during scrolling - - navigation.expand # optimize user experience - - navigation.instant # optimize user experience - - navigation.instant.progress - - navigation.tracking # update address bar - - search.suggest # suggest good completions - - content.code.copy # enable copy to clipboard + # https://www.mkdocs.org/user-guide/configuration/#theme + name: material + icon: + logo: material/book-open-page-variant + # palette: + # scheme: slate + # primary: cyan + features: + - content.tabs.link + - header.autohide # maximum screen space during scrolling + - navigation.expand # optimize user experience + - navigation.instant # optimize user experience + - navigation.instant.progress + - navigation.tracking # update address bar + - search.suggest # suggest good completions + - content.code.copy # enable copy to clipboard # extra css/js see https://www.mkdocs.org/user-guide/customizing-your-theme/ extra_css: [] extra_javascript: [] plugins: - - search - - mknotebooks: - execute: false - - mermaid2: - version: 11.4.1 - - mkdocs_pymdownx_material_extras: - # https://pypi.org/project/mkdocs-pymdownx-material-extras + - search + - mknotebooks: + execute: false + - mermaid2: + version: 11.4.1 + - mkdocs_pymdownx_material_extras: + # https://pypi.org/project/mkdocs-pymdownx-material-extras markdown_extensions: - - md_in_html - - tables - - pymdownx.superfences: - # https://mkdocs-mermaid2.readthedocs.io/en/latest/superfences - # custom code highlighting rules - custom_fences: - - name: mermaid - # disable code highlighting to display diagrams - format: !!python/name:pymdownx.superfences.fence_code_format - class: mermaid + - md_in_html + - tables + - pymdownx.superfences: + # https://mkdocs-mermaid2.readthedocs.io/en/latest/superfences + # custom code highlighting rules + custom_fences: + - name: mermaid + # disable code highlighting to display diagrams + format: !!python/name:pymdownx.superfences.fence_code_format + class: mermaid - # TODO rebuild docs on schema change (https://github.com/dalito/linkml-project-copier/issues/39) - # - gen-files: - # scripts: - # - gen_pages.py # or any other name or path + # TODO rebuild docs on schema change (https://github.com/dalito/linkml-project-copier/issues/39) + # - gen-files: + # scripts: + # - gen_pages.py # or any other name or path watch: - - src/cam_source_enums/schema + - src/cam_source_enums/schema nav: - - Home: index.md - - Schema: elements/index.md - - About: about.md + - Home: index.md + - Term-Weaver: term-expansion.md + - Schema: elements/index.md + - About: about.md exclude_docs: | - /templates-linkml/ + /templates-linkml/ site_url: https://include-dcc.github.io/cam-source-enums repo_url: https://github.com/include-dcc/cam-source-enums From 47a7bde1ba90ce1047ebd5847d8d0db463670314 Mon Sep 17 00:00:00 2001 From: yelenacox Date: Wed, 8 Jul 2026 15:26:47 -0500 Subject: [PATCH 2/2] Clean up linter errors --- .linkml-linter.yaml | 3 +++ justfile | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 .linkml-linter.yaml diff --git a/.linkml-linter.yaml b/.linkml-linter.yaml new file mode 100644 index 0000000..1dcffad --- /dev/null +++ b/.linkml-linter.yaml @@ -0,0 +1,3 @@ +rules: + permissible_values_format: + format: '^[a-zA-Z0-9_\-:]+$' diff --git a/justfile b/justfile index e5dc1e3..ee4f396 100644 --- a/justfile +++ b/justfile @@ -84,7 +84,7 @@ test: _test-schema _test-python _test-examples # Run linting [group('model development')] lint: - uv run linkml-lint {{source_schema_dir}} + uv run linkml-lint --config .linkml-linter.yaml {{source_schema_dir}} # Generate md documentation for the schema and add artifacts [group('model development')]