[docs] Refine docs site

.github/workflows/build-docs.yml

@@ -27,5 +27,5 @@ jobs:
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: pip install mkdocs-material mkdocs-table-reader-plugin
+      - run: pip install mkdocs-material mkdocs-table-reader-plugin pandas
       - run: mkdocs gh-deploy --force

.gitignore

@@ -42,3 +42,8 @@ vignettes/*.pdf
 # schematic-related files
 great_expectations/
 .DS_Store
+**/.DS_Store
+**/**/.DS_Store
+
+# MKDocs
+scripts/__pycache__

docs/index.md

@@ -3,7 +3,9 @@
 </h1>
 
 <p align="center">
-  <img alt="GitHub release (latest by date)" src="https://img.shields.io/github/release/mc2-center/mc2-data-models?label=latest%20release&display_name=release&style=flat-square">
+  <a href="https://github.com/mc2-center/data-models/releases/latest" target="_blank"  rel="noreferrer noopener">
+    <img alt="GitHub release (latest by date)" src="https://img.shields.io/github/release/mc2-center/mc2-data-models?label=latest%20release&display_name=release&style=flat-square">
+  </a>
 </p>
 
 **Welcome!** 👋 Explore metadata terms used by MC<sup>2</sup> Center

docs/model/dataset.md

@@ -0,0 +1 @@
+{{ read_csv('dataset/template.csv') }}

docs/model/education.md

@@ -0,0 +1 @@
+{{ read_csv('education/template.csv') }}

docs/model/grant.md

@@ -0,0 +1 @@
+{{ read_csv('grant/template.csv') }}

docs/model/person.md

@@ -0,0 +1 @@
+{{ read_csv('person/template.csv') }}

docs/model/publication.md

@@ -0,0 +1 @@
+{{ read_csv('publication/template.csv') }}

docs/model/tool.md

@@ -0,0 +1 @@
+{{ read_csv('tool/template.csv') }}

docs/valid_values/all_terms.md

@@ -0,0 +1,4 @@
+!!! note
+    For details and descriptions, please visit the terms by models.
+
+{{ read_csv('../all_valid_values.csv', header=0, names=['Attribute','Term']) }}

docs/valid_values/dataset.md

@@ -0,0 +1,55 @@
+List of standard terms for the [Dataset Data Model](../model/dataset.md).
+
+## Attribute: `Dataset Assay`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/assay.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Dataset File Formats`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('dataset/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Dataset Grant Number`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_number.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Dataset Species`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('dataset/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Dataset Tissue`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tissue.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+
+## Attribute: `Dataset Tumor Type`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tumorType.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>

docs/valid_values/education.md

@@ -0,0 +1,104 @@
+List of standard terms for the [Education Resource Data Model](../model/education.md).
+
+## Attribute: `Resource Access Hazard`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_hazard.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Activity Type`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_activity_type.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Educational Level`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_level.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Grant Number`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_number.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Intended Use`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_intended_use.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Language`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_language.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Media Accessibility`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_accessibility.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Origin Institution`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('institution/institution_name.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Primary Audience`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_primary_audience.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Primary Format`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_primary_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Topic`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('education/ed_topic.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Resource Secondary Topic`
+
+See [Resource Topic](#attribute-resource-topic)

docs/valid_values/grant.md

@@ -0,0 +1,55 @@
+List of standard terms for the [Grant Data Model](../model/grant.md).
+
+
+## Attribute: `Grant Consortium Name`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('consortium/consortium_name.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Grant Institution Alias`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('institution/institution_alias.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Grant Institution Name`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('institution/institution_name.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Grant Number`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_number.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Grant Theme Name`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('theme/theme_name.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Grant Type`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_type.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>

docs/valid_values/person.md

@@ -0,0 +1,45 @@
+List of standard terms for the [Person Data Model](../model/person.md).
+
+## Attribute: `Chair Roles`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('person/chair_roles.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Last Known Institution`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('institution/institution_name.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Person Consortium Name`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('consortium/consortium_name.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Person Grant Number`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_number.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Working Group Participation`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('person/working_group_participation.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>

docs/valid_values/publication.md

@@ -0,0 +1,45 @@
+List of standard terms for the [Publication Data Model](../model/publication.md).
+
+## Attribute: `Publication Accessibility`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('publication/publication_accessibility.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Publication Assay`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/assay.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Publication Grant Number`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('grant/grant_number.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Publication Tissue`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tissue.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Publication Tumor Type`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tumorType.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>