Various issues

COLLABORATORS.md

@@ -1,12 +1,12 @@
-## Welcome to the Kids First Access Model 🚀
+## Welcome to the INCLUDE Access Model 🚀
 
 This repository serves as a downstream model designed to specialize the
 [Common Access Model](https://github.com/include-dcc/common-access-model). A
 pinned version of this upstream model is captured in
 src/kf_access_model/schema/upstream-models/common_access_model*.yaml.
 
 The purpose of this model is to build out a program-specific extension (or
-profile) by importing the core elements and layering the Kids First unique data
+profile) by importing the core elements and layering the INCLUDE unique data
 requirements on top.
 
 ## Key Integration Guidelines

mkdocs.yml

@@ -21,6 +21,33 @@ plugins:
   #     scripts:
   #       - gen_pages.py  # or any other name or path
 
+
+markdown_extensions:
+  - 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
+  # https://facelessuser.github.io/pymdown-extensions/extensions/magiclink/
+  # auto-link HTML, FTP, and email links
+  - pymdownx.magiclink
+  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition
+  # support for call-outs
+  - admonition
+  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#tables
+  # create tables
+  - tables
+  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists
+  # enables use of HTML attributes and CSS classes to applicable elements
+  - attr_list
+  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#markdown-in-html
+  # write markdown inside of HTML
+  - md_in_html
+
+
 watch:
   - src/include_access_model/schema
 

project.justfile

@@ -25,4 +25,4 @@ gen-dbtmodel:
 
 [group('model development')]
 update-cam:
-  uv run update-cam -d src/include_access_model/schema/upstream-models
+  uv run update-cam -l src/include_access_model/schema/include_access_model.yaml -d src/include_access_model/schema/upstream-models

pyproject.toml

@@ -91,3 +91,4 @@ extend-exclude = [
 
 [tool.uv.sources]
 the-caddie = { git = "https://github.com/carrollaboratory/the-caddie" }
+#the-caddie = { path = "/home/torstees/dev/the-caddie" }

src/include_access_model/schema/include_access_model.yaml

@@ -1,11 +1,10 @@
----
 id: https://includedcc.org/include-access-model
 name: include-access-model
 title: INCLUDE DCC Access Model
 description: LinkML Schema for the internal INCLUDE DCC Access Model
 license: MIT
 see_also:
-  - https://includedcc.github.io/include-access-model
+- https://includedcc.github.io/include-access-model
 
 prefixes:
   includedcc: https://includedcc.org/include-access-model/
@@ -85,15 +84,14 @@ default_prefix: includedcc
 default_range: linkml:string
 
 imports:
-  - upstream-models/common_access_model
-
+- upstream-models/common_access_model-0.0.7
 classes:
   IncludeParticipant:
     title: INCLUDE Participant
     description: Information specific to INCLUDE participants
     is_a: Demographics
     slots:
-      - down_syndrome_status
+    - down_syndrome_status
 
 slots:
   down_syndrome_status: