Docs update (#124)

* Create file.md

* Create study.md

* Create valid values file.md

* Add file and study to hooks

* Add study and file markdown to nav

* Create FileView.csv

* Create Study.csv

docs/model/file.md

@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/FileView.csv)
+
+{{ read_csv('file/template.csv') }}

docs/model/study.md

@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/Study.csv)
+
+{{ read_csv('study/template.csv') }}

docs/valid_values/file.md

@@ -0,0 +1,63 @@
+List of standard terms for the [Dataset Sharing Plan Model](../model/file.md).
+
+## Attribute: `File Level`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/processLevel.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File 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: `File Species`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File 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>
+
+
+## Attribute: `File 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: `File Format`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Data Use Codes`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/duo.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>

mkdocs.yml

@@ -14,16 +14,20 @@ nav:
       - Dataset Data Model: model/dataset.md
       - Dataset Sharing Plan: model/DataDSP.md
       - Education Resource Data Model: model/education.md
+      - File Data Model: model/file.md
       - Grant Data Model: model/grant.md
       - Person Data Model: model/person.md
       - Publication Data Model: model/publication.md
+      - Study Data Model: model/study.md
       - Tool Data Model: model/tool.md
+
   - Standard Terms:
     - All terms: valid_values/all_terms.md
     - Terms by model:
       - Dataset: valid_values/dataset.md
       - Dataset Sharing Plan: valid_values/sharingPlans.md
       - Education Resource: valid_values/education.md
+      - File: valid_values/file.md
       - Grant: valid_values/grant.md
       - Person: valid_values/person.md
       - Publication: valid_values/publication.md

scripts/hooks.py

@@ -5,9 +5,11 @@
     "dataset",
     "sharingPlans",
     "education",
+    "file",
     "grant",
     "person",
     "publication",
+    "study",
     "tool",
 ]
 

templates/FileView.csv

@@ -0,0 +1,2 @@
+Component,FileView_id,Biospecimen Key,Study Key,DatasetView Key,Filename,File Alias,File Description,File Design,File Level,File Assay,File Species,File Tumor Type,File Tissue,File Url,File Format,Data Use Codes
+FileView,,,,,,,,,,,,,,,,

templates/Study.csv

@@ -0,0 +1,2 @@
+Component,Study_id,GrantView Key,ProjectView Key,Study Name,Study Description,Study Investigator,PersonView Key,Study Reuse Statement
+Study,,,,,,,,