From 3994df79d06497a16ad7340ecddc619a416af6d7 Mon Sep 17 00:00:00 2001 From: Dorota Jarecka Date: Mon, 17 Jun 2024 12:09:15 -0400 Subject: [PATCH] schenging directory structure for schema, adding mermaid --- .github/workflows/publishdocs.yaml | 4 ++-- docs/{ => schema}/schema.md | 13 ++++++++++--- mkdocs.yml | 3 ++- 3 files changed, 14 insertions(+), 6 deletions(-) rename docs/{ => schema}/schema.md (86%) diff --git a/.github/workflows/publishdocs.yaml b/.github/workflows/publishdocs.yaml index 4aa6a79e7..3c7bdbcca 100644 --- a/.github/workflows/publishdocs.yaml +++ b/.github/workflows/publishdocs.yaml @@ -27,8 +27,8 @@ jobs: - name: Generating docs run: | - gen-doc -d docs/model linkml-schema/reproschema.yaml - gen-erdiagram linkml-schema/reproschema.yaml > docs/model/erdiagram.md + gen-doc -d docs/schema/doc-linkml-autogen linkml-schema/reproschema.yaml + gen-erdiagram linkml-schema/reproschema.yaml > docs/schema/erdiagram-autogen.md - name: Deploy docs uses: mhausenblas/mkdocs-deploy-gh-pages@master diff --git a/docs/schema.md b/docs/schema/schema.md similarity index 86% rename from docs/schema.md rename to docs/schema/schema.md index b0b3c8d38..568c0b131 100644 --- a/docs/schema.md +++ b/docs/schema/schema.md @@ -80,7 +80,14 @@ Protocol The [ReproSchema-UI](https://repronim.org/reproschema-ui) is a prototype implementation of an UI that leverages these different elements of the schema. -## Properties of ReproSchema objects +## ReproSchema Model -- Description of the model automatically generated by LinkML tools is [here](./model/index.md) -- ER diagram to visualize the model is [here](./model/erdiagram.md) +The model was written using a linked data modeling language [LinkML](https://linkml.io/linkml/). + +There are multiple ways of accessing the content +- [The LinkML YAML file that defines the model](https://github.com/ReproNim/reproschema/blob/main/linkml-schema/reproschema.yaml) +- [Automatically generated documentation](./doc-linkml-autogen/index.md) using LinkML tools +- [Automatically generated Entity-Relationship (ER) Diagrams](./erdiagram-autogen.md)) to visualize the model. + +The context was created semi-automatically: the initial version was generated using LinkML tools, +but manual curation was necessary to support all Reeproschema features. diff --git a/mkdocs.yml b/mkdocs.yml index 5721e4d33..b28ca2d0a 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -39,7 +39,7 @@ nav: - Welcome: "index.md" - Introduction: "introduction.md" - Project structure: "project-structure.md" - - Schema: "schema.md" + - Schema: "schema/schema.md" - User Guide: - Create a research protocol: "user-guide/create-new-protocol.md" - Adopt assessments from the library: "user-guide/adopt-assessments.md" @@ -84,3 +84,4 @@ watch: plugins: - search - tags + - mermaid2